Systems Biodynamics Lab


	2010 A synchronized quorum of genetic clocks Tal Danino, Octavio Mondragón-Palomino, Lev Tsimring, Jeff Hasty Nature, 426:326-330 (2010)\| PDF \| 2009 Coherent activation of a synthetic mammalian gene network Diane Longo, Alexander Hoffman, Lev Tsimring, Jeff Hasty Systems and Synthetic Biology, DOI 10.1007/s11693-009-9044-5 (2009)\| PDF \| Cell cycle-dependent variations in protein concentration Natalie Cookson, Scott Cookson, Lev Tsimring, Jeff Hasty Nucleic Acids Research, 1-6 (2009) \| PDF \| The pedestrian watchmaker: Genetic clocks from engineered oscillators Natalie Cookson, Lev Tsimring, Jeff Hasty FEBS Letters, 583 3931–3937 (2009)\| PDF \| Microfluidic devices for measuring gene network dynamics in single cells Matthew Bennett, Jeff Hasty Nature Reviews Genetics, 10(9):628-38 (2009) \| PDF \| Overpowering the component problem Matthew Bennett, Jeff Hasty Nature Biotechnology, 27(5):450-1\| PDF \| Delay-Induced Degrade-and-Fire Oscillations in Small Genetic Circuits William Mather, Matthew Bennett, Jeff Hasty, Lev Tsimring Physical Review Letters, 102(6):068105(4) (2009) \| PDF \| 2008 A fast, robust and tunable synthetic gene oscillator. Jesse Stricker, Scott Cookson, Matthew Bennett, William Mather, Lev Tsimring, Jeff Hasty Nature, 456(7221):516-9 (2008) \| PDF \| See also the News and Views: Synthetic biology: the yin and yang of nature Biomechanical ordering of dense cell populations. Dmitri Volfson, Scott Cookson, Jeff Hasty, Lev Tsimring Proceedings of the National Academy of Sciences, 105(40):15346-51 (2008)\| PDF \| Metabolic gene regulation in a dynamically changing environment Matthew Bennett, Wyoming Lee Pang, Natalie Ostroff, Bridget Baumgartner, Sujata Nayak, Lev Tsimring, Jeff Hasty Nature, 454(7208):1119-22 (2008) \| PDF \| See also the News and Views: Reverse Engineering the Cell A molecular noise generator Ting Lu, Michael Ferry, Ron Weiss, Jeff Hasty Physical Biology, 5(3):36006 (2008) \| PDF \| Athermal Dynamics of Strongly Coupled Stochastic Three-State Oscillators Bastien Fernandez, Lev Tsimring Physical Review Letters, 100(16):165705 (2008) \| PDF \| Regulation of Cell Signaling Dynamics by the Protein Kinase-Scaffold Ste5 Nan Hao, Sujata Nayak, Marcelo Behar, Ryan Shanks, Michal Nagiec, Beverly Errede, Jeff Hasty, Timothy Elston, Henrik Dohlman Molecular Cell, 30(5):539-656 (2008) \| PDF \| Systems Biology: Genome rewired Matthew Bennett, Jeff Hasty Nature, 452(7189):824-5 (2008) \| PDF \| 2007 Phenotypic variability of growing cellular populations Ting Lu, Tongye Shen, Matthew Bennett, Peter Wolynes, Jeff Hasty Proceedings of the National Academy of Sciences, 104:18982–18987 (2007)\| PDF \|
	A synthetic gene network for tuning protein degradation in Saccharomyces cerevisiae Chris Grilly, Jesse Stricker, Wyoming Lee Pang, Matthew Bennett, Jeff Hasty Molecular Systems Biology, msb4100168 (2007) \| PDF \|
	Transient dynamics of genetic regulatory networks Matthew Bennett, Dmitri Volfson, Lev Tsimring, Jeff Hasty Biophysical Journal, 92: 3501-3512 (2007) \| PDF \|
	A DNA methylation–based switch generates bistable gene expression Matthew Bennett, Jeff Hasty Nature Genetics, 39: 146-147 (2007) \| PDF \|
	2006 Dynamics of single-cell gene expression Diane Longo, Jeff Hasty Molecular Systems Biology, msb4100110 (2006) \| PDF \|
	Statistics of cellular signal transduction as a race to the nucleus by multiple random walkers in compartment/phosphorylation space Ting Lu, Tongye Shen, Chenghang Zong, Jeff Hasty, Peter Wolynes Proceedings of the National Academy of Sciences, 103:16752-16757 (2006)\| PDF \|
	Stochastically driven genetic circuits Lev Tsimring, Dmitri Volfson, Jeff Hasty Chaos, 16: 026103 (2006) \| PDF \|
	Imaging gene expression: Tiny signals make a big noise Diane Longo, Jeff Hasty Nature Chemical Biology, 2: 181-182 (2006) \| PDF \|
	Effective temperature in stochastic kinetics and gene networks Ting Lu, Jeff Hasty, Peter Wolynes Biophysical Journal, 91: 84-94 (2006) \| PDF \|
	A bottom-up approach to gene regulation Nicholas Guido, Xiao Wang, David Adalsteinsson, David McMillen, Jeff Hasty, Charles Cantor, Timothy Elston, J.J. Collins Nature, 439: 856-860 (2006) \| PDF \|
	Origins of extrinsic variability in eukaryotic gene expression Dmitri Volfson, Jennifer Marciniak, Natalie Ostroff, William Blake, Lev Tsimring, Jeff Hasty Nature, 439: 861-864 (2006) \| PDF \|
	2005 Monitoring dynamics of single-cell gene expression over multiple cell cycles Scott Cookson, Natalie Ostroff, Wyoming Lee Pang, Dmitri Volfson, Jeff Hasty Molecular Systems Biology, msb4100032 (2005) \| PDF \|
	Delay-induced stochastic oscillations in gene regulation Dmitri Bratsun, Dmitri Volfson, Lev Tsimring, Jeff Hasty Proceedings of the National Academy of Sciences, 102: 14593-14598 (2005)\| PDF \|
	2004 Cellular growth and division in the Gillespie algorithm Ting Lu, Dmitri Volfson, Lev Tsimring, Jeff Hasty IEE Systems Biology, 1:121-127 (2004) \| PDF \|
	2003 Prediction and measurement of an autoregulatory genetic module Farren Isaacs, Jeff Hasty, Charles Cantor, J.J. Collins Proceedings of the National Academy of Sciences, 100 (13) 7714-7719, (2003)\| PDF \|
	Derivation of the governing equations for "Prediction and measurement of an autoregulatory genetic module" (supplement) Farren Isaacs, Jeff Hasty, Charles Cantor, J.J. Collins \| PDF \|
	Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling Jesper Tegner, Stephen Yeung, Jeff Hasty, J.J. Collins Proceedings of the National Academy of Sciences,100 (10): 5944-5949 (2003)\| PDF \|
	2002 Design then mutate Jeff Hasty Proceedings of the National Academy of Sciences, 99 (26): 16516-16518 (2002)\| PDF \|
	Engineered gene circuits Jeff Hasty, David McMillen, J.J. Collins Nature, 420 (6912): 224-230 (2002) \| PDF \|
	Translating the noise Jeff Hasty, J.J. Collins Nature Genetics, 31 (1): 13-4 (2002) \| PDF \|
	A synthetic gene network for entraining and amplifying cellular oscillations Jeff Hasty, Milos Dolnik, Vivi Rottschafer, J.J. Collins Physical Review Letters, 88 (14): art. no. 148101 (2002) \| PDF \|
	Synchronizing genetic relaxation oscillators by intercell signalling David McMillen, Nancy Kopell, Jeff Hasty, J.J. Collins Proceedings of the National Academy of Sciences, 99 (2): 679-684 (2002) \| PDF \|
	2001 Complex ligand-protein systems: a globally convergent iterative method for the n x m case J Pradines, Jeff Hasty, K Pakdaman Journal of Mathematical Biology, 43 (4): 313-324 (2001)
	Wavelets of excitibility in sensory neurons Jeff Hasty, J.J. Collins, Kurt Wiesenfeld, Peter Grigg Journal of Neurophysiology, 86 (4): 2097-2101 (2001) \| PDF \|
	Protein interactions - Unspinning the web Jeff Hasty, J.J. Collins Nature, 411 (6833): 30-31 (2001) \| PDF \|
	Computational studies of gene regulatory networks: in numero molecular biology Jeff Hasty, David McMillen, Farren Isaacs, J.J. Collins Nature Reviews Genetics, 2 (4): 268-279 (2001) \| PDF \|
	Designer gene networks: Towards fundamental cellular control Jeff Hasty, Farren Isaacs, Milos Dolnik, David McMillen, J.J. Collins Chaos, 11 (1): 207-220 (2001) \| PDF \|
	2000 Noise-based switches and amplifiers for gene expression Jeff Hasty, Joel Pradines, Milos Dolnik, J.J. Collins Proceedings of the National Academy of Sciences, 97 (5): 2075-2080 (2000)\| PDF \|
	1998 Renormalization group for directed sandpile models Jeff Hasty, Kurt Wiesenfeld Physical Review Letters, 81 (8): 1722-1725 (1998) \| PDF \|
	1997 Renormalization of one-dimensional avalanche models Jeff Hasty, Kurt Wiesenfeld Journal of Statistical Physics, 86 (5-6): 11/79-1201 (1997)

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	2010 A synchronized quorum of genetic clocks Tal Danino, Octavio Mondragón-Palomino, Lev Tsimring, Jeff Hasty Nature, 426:326-330 (2010)\| PDF \| 2009 Coherent activation of a synthetic mammalian gene network Diane Longo, Alexander Hoffman, Lev Tsimring, Jeff Hasty Systems and Synthetic Biology, DOI 10.1007/s11693-009-9044-5 (2009)\| PDF \| Cell cycle-dependent variations in protein concentration Natalie Cookson, Scott Cookson, Lev Tsimring, Jeff Hasty Nucleic Acids Research, 1-6 (2009) \| PDF \| The pedestrian watchmaker: Genetic clocks from engineered oscillators Natalie Cookson, Lev Tsimring, Jeff Hasty FEBS Letters, 583 3931–3937 (2009)\| PDF \| Microfluidic devices for measuring gene network dynamics in single cells Matthew Bennett, Jeff Hasty Nature Reviews Genetics, 10(9):628-38 (2009) \| PDF \| Overpowering the component problem Matthew Bennett, Jeff Hasty Nature Biotechnology, 27(5):450-1\| PDF \| Delay-Induced Degrade-and-Fire Oscillations in Small Genetic Circuits William Mather, Matthew Bennett, Jeff Hasty, Lev Tsimring Physical Review Letters, 102(6):068105(4) (2009) \| PDF \| 2008 A fast, robust and tunable synthetic gene oscillator. Jesse Stricker, Scott Cookson, Matthew Bennett, William Mather, Lev Tsimring, Jeff Hasty Nature, 456(7221):516-9 (2008) \| PDF \| See also the News and Views: Synthetic biology: the yin and yang of nature Biomechanical ordering of dense cell populations. Dmitri Volfson, Scott Cookson, Jeff Hasty, Lev Tsimring Proceedings of the National Academy of Sciences, 105(40):15346-51 (2008)\| PDF \| Metabolic gene regulation in a dynamically changing environment Matthew Bennett, Wyoming Lee Pang, Natalie Ostroff, Bridget Baumgartner, Sujata Nayak, Lev Tsimring, Jeff Hasty Nature, 454(7208):1119-22 (2008) \| PDF \| See also the News and Views: Reverse Engineering the Cell A molecular noise generator Ting Lu, Michael Ferry, Ron Weiss, Jeff Hasty Physical Biology, 5(3):36006 (2008) \| PDF \| Athermal Dynamics of Strongly Coupled Stochastic Three-State Oscillators Bastien Fernandez, Lev Tsimring Physical Review Letters, 100(16):165705 (2008) \| PDF \| Regulation of Cell Signaling Dynamics by the Protein Kinase-Scaffold Ste5 Nan Hao, Sujata Nayak, Marcelo Behar, Ryan Shanks, Michal Nagiec, Beverly Errede, Jeff Hasty, Timothy Elston, Henrik Dohlman Molecular Cell, 30(5):539-656 (2008) \| PDF \| Systems Biology: Genome rewired Matthew Bennett, Jeff Hasty Nature, 452(7189):824-5 (2008) \| PDF \| 2007 Phenotypic variability of growing cellular populations Ting Lu, Tongye Shen, Matthew Bennett, Peter Wolynes, Jeff Hasty Proceedings of the National Academy of Sciences, 104:18982–18987 (2007)\| PDF \|
	A synthetic gene network for tuning protein degradation in Saccharomyces cerevisiae Chris Grilly, Jesse Stricker, Wyoming Lee Pang, Matthew Bennett, Jeff Hasty Molecular Systems Biology, msb4100168 (2007) \| PDF \|
	Transient dynamics of genetic regulatory networks Matthew Bennett, Dmitri Volfson, Lev Tsimring, Jeff Hasty Biophysical Journal, 92: 3501-3512 (2007) \| PDF \|
	A DNA methylation–based switch generates bistable gene expression Matthew Bennett, Jeff Hasty Nature Genetics, 39: 146-147 (2007) \| PDF \|
	2006 Dynamics of single-cell gene expression Diane Longo, Jeff Hasty Molecular Systems Biology, msb4100110 (2006) \| PDF \|
	Statistics of cellular signal transduction as a race to the nucleus by multiple random walkers in compartment/phosphorylation space Ting Lu, Tongye Shen, Chenghang Zong, Jeff Hasty, Peter Wolynes Proceedings of the National Academy of Sciences, 103:16752-16757 (2006)\| PDF \|
	Stochastically driven genetic circuits Lev Tsimring, Dmitri Volfson, Jeff Hasty Chaos, 16: 026103 (2006) \| PDF \|
	Imaging gene expression: Tiny signals make a big noise Diane Longo, Jeff Hasty Nature Chemical Biology, 2: 181-182 (2006) \| PDF \|
	Effective temperature in stochastic kinetics and gene networks Ting Lu, Jeff Hasty, Peter Wolynes Biophysical Journal, 91: 84-94 (2006) \| PDF \|
	A bottom-up approach to gene regulation Nicholas Guido, Xiao Wang, David Adalsteinsson, David McMillen, Jeff Hasty, Charles Cantor, Timothy Elston, J.J. Collins Nature, 439: 856-860 (2006) \| PDF \|
	Origins of extrinsic variability in eukaryotic gene expression Dmitri Volfson, Jennifer Marciniak, Natalie Ostroff, William Blake, Lev Tsimring, Jeff Hasty Nature, 439: 861-864 (2006) \| PDF \|
	2005 Monitoring dynamics of single-cell gene expression over multiple cell cycles Scott Cookson, Natalie Ostroff, Wyoming Lee Pang, Dmitri Volfson, Jeff Hasty Molecular Systems Biology, msb4100032 (2005) \| PDF \|
	Delay-induced stochastic oscillations in gene regulation Dmitri Bratsun, Dmitri Volfson, Lev Tsimring, Jeff Hasty Proceedings of the National Academy of Sciences, 102: 14593-14598 (2005)\| PDF \|
	2004 Cellular growth and division in the Gillespie algorithm Ting Lu, Dmitri Volfson, Lev Tsimring, Jeff Hasty IEE Systems Biology, 1:121-127 (2004) \| PDF \|
	2003 Prediction and measurement of an autoregulatory genetic module Farren Isaacs, Jeff Hasty, Charles Cantor, J.J. Collins Proceedings of the National Academy of Sciences, 100 (13) 7714-7719, (2003)\| PDF \|
	Derivation of the governing equations for "Prediction and measurement of an autoregulatory genetic module" (supplement) Farren Isaacs, Jeff Hasty, Charles Cantor, J.J. Collins \| PDF \|
	Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling Jesper Tegner, Stephen Yeung, Jeff Hasty, J.J. Collins Proceedings of the National Academy of Sciences,100 (10): 5944-5949 (2003)\| PDF \|
	2002 Design then mutate Jeff Hasty Proceedings of the National Academy of Sciences, 99 (26): 16516-16518 (2002)\| PDF \|
	Engineered gene circuits Jeff Hasty, David McMillen, J.J. Collins Nature, 420 (6912): 224-230 (2002) \| PDF \|
	Translating the noise Jeff Hasty, J.J. Collins Nature Genetics, 31 (1): 13-4 (2002) \| PDF \|
	A synthetic gene network for entraining and amplifying cellular oscillations Jeff Hasty, Milos Dolnik, Vivi Rottschafer, J.J. Collins Physical Review Letters, 88 (14): art. no. 148101 (2002) \| PDF \|
	Synchronizing genetic relaxation oscillators by intercell signalling David McMillen, Nancy Kopell, Jeff Hasty, J.J. Collins Proceedings of the National Academy of Sciences, 99 (2): 679-684 (2002) \| PDF \|
	2001 Complex ligand-protein systems: a globally convergent iterative method for the n x m case J Pradines, Jeff Hasty, K Pakdaman Journal of Mathematical Biology, 43 (4): 313-324 (2001)
	Wavelets of excitibility in sensory neurons Jeff Hasty, J.J. Collins, Kurt Wiesenfeld, Peter Grigg Journal of Neurophysiology, 86 (4): 2097-2101 (2001) \| PDF \|
	Protein interactions - Unspinning the web Jeff Hasty, J.J. Collins Nature, 411 (6833): 30-31 (2001) \| PDF \|
	Computational studies of gene regulatory networks: in numero molecular biology Jeff Hasty, David McMillen, Farren Isaacs, J.J. Collins Nature Reviews Genetics, 2 (4): 268-279 (2001) \| PDF \|
	Designer gene networks: Towards fundamental cellular control Jeff Hasty, Farren Isaacs, Milos Dolnik, David McMillen, J.J. Collins Chaos, 11 (1): 207-220 (2001) \| PDF \|
	2000 Noise-based switches and amplifiers for gene expression Jeff Hasty, Joel Pradines, Milos Dolnik, J.J. Collins Proceedings of the National Academy of Sciences, 97 (5): 2075-2080 (2000)\| PDF \|
	1998 Renormalization group for directed sandpile models Jeff Hasty, Kurt Wiesenfeld Physical Review Letters, 81 (8): 1722-1725 (1998) \| PDF \|
	1997 Renormalization of one-dimensional avalanche models Jeff Hasty, Kurt Wiesenfeld Journal of Statistical Physics, 86 (5-6): 11/79-1201 (1997)