Collins Lab:Reprints

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'''Synthetic Biology'''
 
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Lu TK and Collins JJ. Dispersing biofilms with engineered enzymatic bacteriophage. Proceedings of the National Academy of Sciences USA published June 25, 2007, 10.1073/pnas.0704624104.                                       [[http://www.pnas.org/cgi/reprint/0704624104v1 pdf file]]
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# Brynildsen MP and Collins JJ. Systems biology makes it personal. Molecular Cell 34: 137-138 (2009). [http://www.bu.edu/abl/files/molecularcell_mark.pdf] <BR> 

 +
# Camacho DM and Collins JJ. Systems biology strikes gold. Cell 137: 24-26 (2009). [http://www.bu.edu/abl/files/cell_camacho.pdf] <BR> 

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# Schembri F, Sridhar S, Perdomo C, Gustafson AM, Zhang X, Ergun A, Lu J, Liu G, Zhang X, Bowers J, Vaziri C, Ott K, Sensinger K, Collins JJ, Brody JS, Getts R, Lenburg ME and Spira A. MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium. Proceedings of the National Academy of Sciences USA 106: 2319-2324 (2009). [http://www.bu.edu/abl/files/pnas_spira.pdf] <BR> 

 +
# Lorenz DR, Cantor CR and Collins JJ. A network biology approach to aging in yeast. Proceedings of the National Academy of Sciences USA 106: 1145-1150 (2009). [http://www.bu.edu/abl/files/pnas_lorenz.pdf] <BR> 

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# Dwyer DJ, Kohanski MA and Collins JJ. Networking opportunities for bacteria. Cell 135: 1153-1156 (2008). [http://www.bu.edu/abl/files/cell_dwyer.pdf] <BR> 

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# Kohanski MA, Dwyer DJ, Wierzbowski J, Cottarel G and Collins JJ. Mistranslation of membrane proteins and two-component system activation trigger antibiotic-mediated cell death. Cell 135: 679-690 (2008). [http://www.bu.edu/abl/files/cell_kohanski2.pdf] <BR> 

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# Heng TS, Painter MW, Elpek K, Lukacs-Kornek V, Mauermann N, Turley SJ, Koller D, Kim FS, Wagers AJ, Asinovski N, Davis S, Fassett M, Feuerer M, Gray DH, Haxhinasto S, Hill JA, Hyatt G, Laplace C, Leatherbee K, Mathis D, Benoist C, Jianu R, Laidlaw DH, Best JA, Knell J, Goldrath AW, Jarjoura J, Sun JC, Zhu Y, Lanier LL, Ergun A, Li Z, Collins JJ, Shinton SA, Hardy RR, Friedline R, Sylvia K and Kang J. The Immunological Genome Project: networks of gene expression in immune cells.  Nature Immunolology 9: 1091-1094 (2008). [http://www.bu.edu/abl/files/nature_immunology.pdf] <BR> 

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# Ellis T, Wang X and Collins JJ. Gene regulation: hacking the network on a sugar high. Molecular Cell 30: 1-2 (2008). [http://www.bu.edu/abl/files/molecularcell_ellis2.pdf] <BR> 

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# Kohanski MA, Dwyer DJ, Hayete B, Lawrence CA and Collins JJ. A common mechanism of cellular death induced by bactericidal antibiotics. Cell 130: 797-810 (2007). [http://www.bu.edu/abl/files/cell_kohanski.pdf] <BR> 

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# Dwyer DJ, Kohanski MA, Hayete B and Collins JJ. Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli. Molecular Systems Biology 3: 91 (2007). [http://www.bu.edu/abl/files/msb_dwyer.pdf] <BR>

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# Ergun A, Lawrence CA, Kohanski MA, Brennan TA and Collins JJ. A network biology approach to prostate cancer. Molecular Systems Biology 3: 82 (2007). [http://www.bu.edu/abl/files/msb_ergun.pdf] <BR>

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# Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ and Gardner TS. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biology 5(1): e8 (2007). [http://www.bu.edu/abl/files/plos_faith.pdf] <BR> 

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# Hayete B, Gardner TS and Collins JJ. Size matters: network inference tackles the genome scale. Molecular Systems Biology 3: 77 (2007). [http://www.bu.edu/abl/files/msb_hayete.pdf] <BR> 

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# di Bernardo D, Thompson MJ, Gardner TS, Chobot SE, Eastwood EL, Wojtovich AP, Elliot SJ, Schaus SE and Collins JJ. Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nature Biotechnology 23: 377-383 (2005). [http://www.bu.edu/abl/files/nbt_dibernardo.pdf] <BR>

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# Gardner TS, Shimer S and Collins JJ. Inferring microbial genetic networks. ASM News 70: 121-126 (2004). [http://www.bu.edu/abl/pdf/asm_gardner.pdf] <BR>

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# Gardner TS, Bernardo D, Lorenz D and Collins JJ. Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301: 102-105 (2003). [http://www.bu.edu/abl/pdf/gardner2003.pdf] <BR>

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# Tegner J, Yeung MKS, Hasty J and Collins JJ. Reverse engineering gene networks - Integrating genetic perturbations with dynamical modeling. Proceedings of the National Academy of Sciences USA 100: 5944-5949 (2003). [http://www.bu.edu/abl/pdf/tegner2003.pdf] <BR>

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# Yeung MKS, Tegner J and Collins JJ. Reverse engineering gene networks using singular value decomposition and robust regression. Proceedings of the National Academy of Sciences USA 99: 6163-6168 (2002). [http://www.bu.edu/abl/pdf/yeung2002.pdf] <BR>

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# Hasty J and Collins JJ. Protein interactions: unspinning the web. Nature 411: 30-31 (2001). [http://www.bu.edu/abl/files/unspinning_the_web.pdf] <BR>

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<BR> SYNTHETIC BIOLOGY <BR>
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Balazsi G and Collins JJ. Taking the inventory inside single cells. Nat Chem Biol 3(3): 141-2 (2007).
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# Friedland AE, Lu TK, Wang X, Shi D, Church G and Collins JJ. Synthetic gene networks that count. Science 324: 1199-1202 (2009). [http://www.bu.edu/abl/files/science_friedland.pdf] <BR>

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# Ellis T, Wang X and Collins JJ. Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nature Biotechnology 27: 465-471 (2009). [http://www.bu.edu/abl/files/naturebiotech_ellis.pdf] <BR> 

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# Lu TK and Collins JJ. Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy. Proceedings of the National Academy of Sciences USA 106: 4629-4634 (2009). [http://www.bu.edu/abl/files/pnas_lu2.pdf] <BR> 

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# Kohanski MA and Collins JJ. Rewiring bacteria, two components at a time. Cell 133: 947-948 (2008). [http://www.bu.edu/abl/files/cell_preview_kohanski.pdf] <BR> 

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# Guido NJ, Lee P, Wang X, Elston TC and Collins JJ. A pathway and genetic factors contributing to elevated gene expression noise in stationary phase. Biophysical Journal 93: L55-L57 (2007). [http://www.bu.edu/abl/files/biophysj_guido%5B1%5D.pdf] <BR> 

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# Deans TL, Cantor CR and Collins JJ. A tunable genetic switch based on RNAi and repressor proteins for regulating gene expression in mammalian cells. Cell 130: 363-372 (2007). [http://www.bu.edu/abl/files/cell_deans.pdf] <BR> 

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# Murphy KF, Balazsi G and Collins JJ. Combinatorial promoter design for engineering noisy gene expression. Proceedings of the National Academy of Sciences USA 104: 12726-12731 (2007). [http://www.bu.edu/abl/files/pnas_murphy.pdf] <BR> 

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# Lu TK and Collins JJ. Dispersing biofilms with engineered enzymatic bacteriophage. Proceedings of the National Academy of Sciences USA 104: 11197-11202 (2007). [http://www.bu.edu/abl/files/pnas_lu.pdf] <BR> 

 +
# Balazsi G and Collins JJ. Taking the inventory inside single cells. Nature Chemical Biology 3: 141-142 (2007). [http://www.bu.edu/abl/files/nchembio0307-141.pdf] <BR>

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# Blake WJ, Balazsi G, Kohanski MA, Isaacs FJ, Murphy KF, Kuang Y, Cantor CR, Collins JJ. Phenotypic consequences of promoter-mediated transcriptional noise. Molecular Cell 24: 853-865 (2006). [http://www.bu.edu/abl/files/molecularcell_blake.pdf] <BR>

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# Baker D, Church G, Collins J, Endy D, Jacobson J, Keasling J, Modrich P, Smolke C, Weiss R. Engineering life: building a FAB for biology. Scientific American 294: 44-51 (2006). [http://www.bu.edu/abl/files/BioFab0606.pdf] <BR>

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# Isaacs FJ, Dwyer DJ and Collins JJ. RNA synthetic biology. Nature Biotechnology 24: 545-554 (2006). [http://www.bu.edu/abl/files/naturebiotech_isaacs.pdf] <BR> 

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# Guido NJ, Wang X, Adalsteinsson D, McMillen D, Hasty J, Cantor CR, Elston TC and Collins JJ. A bottom-up approach to gene regulation. Nature 439: 856-860 (2006). [http://www.bu.edu/abl/files/nature_guido.pdf] <BR> 

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# Blake WJ and Collins JJ. And the noise played on: stochastic gene expression and HIV-1 infection. Cell 122: 147-155 (2005). [http://www.bu.edu/abl/files/cell_blake.pdf] <BR> 

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# Kaern M, Elston TC, Blake WJ, and Collins JJ. Stochasticity in gene expression: from theories to phenotypes. Nature Reviews Genetics 6: 451-464 (2005). [http://www.bu.edu/abl/files/stochasticity%20in%20gene.pdf] <BR>

 +
# Isaacs FJ, Blake WJ and Collins JJ. Signal processing in single cells. Science 307: 1886-1888 (2005). [http://www.bu.edu/abl/files/science_isaacs.pdf] <BR> 

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# Isaacs FJ and Collins JJ. Plug-and-play with RNA. Nature Biotechnology 23: 306-307 (2005). [http://www.bu.edu/abl/files/nbt_isaacs_nv.pdf] <BR>

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# Isaacs FJ, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR and Collins JJ. Engineered riboregulators enable post-transcriptional control of gene expression. Nature Biotechnology 22: 841-847 (2004). [http://www.bu.edu/abl/pdf/isaacs2004.pdf] <BR>

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# Kobayashi H, Kaern M, Araki M, Chung K, Gardner TS, Cantor CR and Collins JJ. Programmable cells: Interfacing natural and engineered gene networks. Proceedings of the National Academy of Sciences USA 101: 8414-8419 (2004). [http://www.bu.edu/abl/pdf/pnas_kobayashi.pdf] <BR>

 +
# Mason J, Linsay P, Collins JJ and Glass L. Evolving complex dynamics in electronic models of genetic networks. Chaos 14: 707-715 (2004). [http://www.bu.edu/abl/pdf/chaos_mason.pdf] <BR> 

 +
# Isaacs FJ, Hasty J, Cantor CR and Collins JJ. Prediction and measurement of an autoregulatory genetic module. Proceedings of the National Academy of Sciences USA 100: 7714-7719 (2003). [http://www.bu.edu/abl/pdf/isaacs2003.pdf] <BR>

 +
# Blake WJ, Kaern M, Cantor CR and Collins JJ. Noise in eukaryotic gene expression. Nature 422: 633-637 (2003). [http://www.bu.edu/abl/pdf/blake2003.pdf?file=/nature/journal/v422/n6932/full/nature01546_fs.html&content_filetype=PDF] <BR> 

 +
# Kaern M, Blake WJ and Collins JJ. The engineering of gene regulatory networks. Annual Review of Biomedical Engineering 5: 179-206 (2003). [http://www.bu.edu/abl/pdf/kaern2003.pdf] <BR>

 +
# Hasty J, McMillen D and Collins JJ. Engineered gene circuits. Nature 420: 224-230 (2002). [http://www.bu.edu/abl/pdf/hasty2002.pdf?file=/nature/journal/v420/n6912/full/nature01257_fs.html&content_filetype=PDF] <BR> 

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# Hasty J, Dolnik M, Rottschafer V and Collins JJ. A synthetic gene network for entraining and amplifying cellular oscillations. Physical Review Letters 88: 148101 (2002). [http://www.bu.edu/abl/pdf/hasty2002prl.pdf?filetype=pdf&id=PRLTAO000088000014148101000001&idtype=cvips] <BR> 

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# McMillen D, Kopell N, Hasty J and Collins JJ. Synchronizing genetic relaxation oscillators with intercell signaling. Proceedings of the National Academy of Sciences USA 99: 679-684 (2002). [http://www.bu.edu/abl/pdf/mcmillen2002.pdf] <BR> 

 +
# Hasty J and Collins JJ. Translating the noise. Nature Genetics 31: 13-14 (2002). [http://www.bu.edu/abl/files/translating_the_noise.pdf] <BR>

 +
# Hasty J, McMillen D, Isaacs F and Collins JJ. Computational studies of gene regulatory networks: In numero molecular biology. Nature Reviews Genetics 2: 268-279 (2001). [http://www.bu.edu/abl/pdf/hasty2001nature.pdf?file=/nrg/journal/v2/n4/full/nrg0401_268a_fs.html&filetype=PDF] <BR> 

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# Hasty J, Isaacs F, Dolnik M, McMillen D and Collins JJ. Designer gene networks: Towards fundamental cellular control. CHAOS 11: 207-220 (2001). [http://www.bu.edu/abl/pdf/hasty2001chaos.pdf] <BR> 

 +
# Gardner TS and Collins JJ. Neutralizing noise in gene networks. Nature 405: 520-521 (2000). [http://www.bu.edu/abl/files/neutralizing_noise_in.pdf] <BR>

 +
# Hasty J, Pradines J, Dolnik M and Collins JJ. Noise-based switches and amplifiers for gene expression. Proceedings of the National Academy of Sciences USA 97: 2075-2080 (2000). [http://www.bu.edu/abl/pdf/hasty2000pnas.pdf] <BR> 

 +
# Gardner TS, Cantor CR and Collins JJ. Construction of a genetic toggle switch in Escherichia coli. Nature 403: 339-342 (2000). [http://www.bu.edu/abl/pdf/gardner2001nature.pdf?file=/nature/journal/v403/n6767/full/403339a0_fs.html&content_filetype=PDF] <BR>

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<BR> NOISE-ENHANCED SENSORIMOTOR FUNCTION <BR>
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Blake WJ, Balazsi G, Kohanski MA, Isaacs FJ, Murphy KF, Kuang Y, Cantor CR, Walt DR, and Collins JJ. Phenotypic consequences of promoter-mediated transcriptional noise. Molecular Cell 24: 853-865 (2006).  [[http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WSR-4MP08C5-7-G&_cdi=7053&_user=489277&_orig=search&_coverDate=12%2F28%2F2006&_sk=999759993&view=c&wchp=dGLbVtz-zSkzS&md5=203ce4295643db6e8b22e32bc51380e9&ie=/sdarticle.pdf pdf file]]
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# Priplata AA, Patritti BL, Niemi JB, Hughes R, Gravelle DC, Lipsitz LA, Veves A, Stein J, Bonato P and Collins JJ. Noise-enhanced balance control in patients with diabetes and patients with stroke. Annals of Neurology 59: 4-12 (2006). [http://www.bu.edu/abl/files/fulltext.pdf] <BR>

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# Harry JD, Niemi JB, Priplata AA and Collins JJ. Balancing act. IEEE Spectrum, April: 36-41 (2005). [http://www.bu.edu/abl/files/] <BR>ieeespectrum_harry.pdf] <BR> 

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# Priplata AA, Niemi JB, Harry JD, Lipsitz LA and Collins JJ. Vibrating insoles and balance control in elderly people. The Lancet 362: 1123-1124 (2003). [http://www.bu.edu/abl/pdf/priplata2003lancet.pdf] <BR> 

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Baker D, Church G, Collins J, Endy D, Jacobson J, Keasling J, Modrich P, Smolke C, Weiss R. Engineering life: building a FAB for biology. Scientific American 294: 44-51 (2006). [[http://www.bu.edu/abl/files/BioFab0606.pdf pdf file]]
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# Collins JJ, Priplata AA, Gravelle DC, Niemi J, Harry J and Lipsitz LA. Noise-enhanced human sensorimotor function. IEEE Engineering in Medicine and Biology Magazine 22: 76-83 (2003). [http://www.bu.edu/abl/pdf/collins2003ieee.pdf] <BR>

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# Priplata AA, Niemi J, Salen M, Harry J, Lipsitz LA and Collins JJ. Noise-enhanced human balance control. Physical Review Letters 89: 238101 (2002). [http://www.bu.edu/abl/pdf/priplata2002prl.pdf?filetype=pdf&id=PRLTAO000089000023238101000001&idtype=cvips] <BR> 

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# Gravelle DC, Laughton CA, Dhruv NT, Katdare KD, Niemi JB, Lipsitz LA and Collins JJ. Noise-enhanced balance control in older adults. Neuroreport 13: 1853-1856 (2002). [http://www.bu.edu/abl/pdf/gravelle2002.pdf] <BR> 

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Isaacs FJ, Dwyer DJ and Collins JJ. RNA synthetic biology. Nature Biotechnology 24: 545-554 (2006). [[http://www.bu.edu/abl/files/naturebiotech_isaacs.pdf pdf file]]
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# Dhruv NT, Niemi JB, Harry JD, Lipsitz LA and Collins JJ. Enhancing tactile sensation in older adults with electrical noise stimulation. Neuroreport 13: 597-600 (2002). [http://www.bu.edu/abl/pdf/dhruv2002.pdf] <BR> 

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# Liu W, Lipsitz LA, Montero-Odasso M, Bean J, Kerrigan DC and Collins JJ. Noise-enhanced vibrotactile sensitivity in older adults and patients with stroke and patients with diabetic neuropathy. Archives of Physical Medicine and Rehabilitation 83: 171-176 (2002). [http://www.bu.edu/abl/pdf/liu2002.pdf] <BR>

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# Nozaki D, Collins JJ and Yamamoto Y. Mechanism of stochastic resonance enhancement in neuronal models driven by 1/f noise. Physical Review E 60: 4637-4644 (1999). [http://www.bu.edu/abl/files/mechanism_of_stochastic.pdf] <BR>

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Guido NJ, Wang X, Adalsteinsson D, McMillen D, Hasty J, Cantor CR, Elston TC and Collins JJ. A bottom-up approach to gene regulation. Nature 439: 856-860 (2006). [[http://www.bu.edu/abl/files/nature_guido.pdf pdf file]]
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# Pradines JR, Osipov GV and Collins JJ. Coherence resonance in excitable and oscillatory systems: the essential role of slow and fast dynamics.  Physical Review E 60: 6407-6410 (1999). [http://www.bu.edu/abl/files/coherence_resonance_in.pdf] <BR>

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# Neiman A, Schimansky-Geier L, Moss F, Shulgin B and Collins JJ. Synchronization of noisy systems by stochastic signals. Physical Review E 60: 284-292 (1999). [http://www.bu.edu/abl/files/synchronization_of_noisy.pdf] <BR>

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# Nozaki D, Mar DJ, Grigg P and Collins JJ. Effects of colored noise on stochastic resonance in sensory neurons. Physical Review Letters 82: 2402-2405 (1999). [http://www.bu.edu/abl/files/effects_of_colored.pdf] <BR>

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Blake WJ and Collins JJ. And the noise played on: stochastic gene expression and HIV-1 infection. Cell 122: 147-155 (2005).  [[http://www.bu.edu/abl/files/cell_blake.pdf pdf file]]
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# Collins JJ. Fishing for function in noise. Nature 402: 241-242 (1999). [http://www.bu.edu/abl/files/fishing_for_function.pdf] <BR>

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# Suki B, Alencar AM, Sujeer MK, Lutchen KR, Collins JJ, Andrade JS, Ingenito EP, Zapperi S and Stanley HE. Life-support system benefits from noise. Nature 393: 127-128 (1998). [http://www.bu.edu/abl/files/life_support_system.pdf] <BR>

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# Richardson KA, Imhoff TT, Grigg P and Collins JJ. Using electrical noise to enhance the ability of humans to detect subthreshold mechanical cutaneous stimuli. CHAOS 8: 599-603 (1998). [http://www.bu.edu/abl/files/using_electrical_noise.pdf] <BR>

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Kaern M, Elston TC, Blake WJ, and Collins JJ. Stochasticity in gene expression: from theories to phenotypes. Nature Reviews Genetics 6: 451-464 (2005). [[http://www.bu.edu/abl/files/stochasticity%20in%20gene.pdf pdf file]]
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# Chow CC, Imhoff TT and Collins JJ. Enhancing aperiodic stochastic resonance through noise modulation. CHAOS 8: 616-620 (1998). [http://www.bu.edu/abl/files/enhancing_aperiodic_stochastic.pdf] <BR>

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# Gailey PC, Neiman A, Collins JJ and Moss F. Stochastic resonance in ensembles of nondynamical elements: the role of internal noise. Physical Review Letters 79: 4701-4704 (1997). [http://www.bu.edu/abl/files/stochastic_resonance_in.pdf] <BR>

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# Collins JJ, Imhoff TT and Grigg P. Noise-mediated enhancements and decrements in human tactile sensation. Physical Review E 56: 923-926 (1997). [http://www.bu.edu/abl/files/noise_mediated_enhancements.pdf] <BR>

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Isaacs FJ, Blake WJ and Collins JJ. Signal processing in single cells. Science 307: 1886-1888 (2005). [[http://www.bu.edu/abl/files/science_isaacs.pdf pdf file]]
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# Cordo P, Inglis JT, Verschueren S, Collins JJ, Merfeld DM, Rosenblum S, Buckley S and Moss F. Noise in human muscle spindles. Nature 383: 769-770 (1996). [http://www.bu.edu/abl/files/noise_in_human.pdf] <BR>

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# Collins JJ, Imhoff TT and Grigg P. Noise-enhanced tactile sensation. Nature 383: 770 (1996). [http://www.bu.edu/abl/files/noise_enhanced_tactile.pdf] <BR>

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# Collins JJ, Imhoff TT and Grigg P. Noise-enhanced information transmission in rat SA1 cutaneous mechanoreceptors via aperiodic stochastic resonance. Journal of Neurophysiology 76: 642-645 (1996). [http://www.bu.edu/abl/files/noise_enhanced_information.pdf] <BR>

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Isaacs FJ and Collins JJ. Plug-and-play with RNA. Nature Biotechnology 23: 306-307 (2005).  [[http://www.bu.edu/abl/files/nbt_isaacs_nv.pdf pdf file]]
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# Collins JJ, Chow CC, Capela AC and Imhoff TT. Aperiodic stochastic resonance. Physical Review E 54: 5575-5584 (1996). [http://www.bu.edu/abl/files/aperiodic_stochastic_resonance.pdf] <BR>

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# Heneghan C, Chow CC, Collins JJ, Imhoff TT, Lowen SB and Teich MC. Information measures quantifying aperiodic stochastic resonance. Physical Review E 54: R2228-R2231 (1996). [http://www.bu.edu/abl/files/information_measures_quantifying.pdf] <BR>

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# Collins JJ, Chow CC and Imhoff TT. Aperiodic stochastic resonance in excitable systems. Physical Review E 52: R3321-R3324 (1995). [http://www.bu.edu/abl/files/aps_in_excitable.pdf] <BR>

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Isaacs FJ, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR and Collins JJ. Engineered riboregulators enable post-transcriptional control of gene expression. Nature Biotechnology 22: 841-847 (2004). [[http://www.bu.edu/abl/pdf/isaacs2004.pdf pdf file]]
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# Collins JJ, Chow CC and Imhoff TT. Stochastic resonance without tuning. Nature 376: 236-238 (1995). [http://www.bu.edu/abl/files/stochastic_resonance_without.pdf] <BR>

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Kobayashi H, Kaern M, Araki M, Chung K, Gardner TS, Cantor CR and Collins JJ. Programmable cells: Interfacing natural and engineered gene networks. Proceedings of the National Academy of Sciences USA 101: 8414-8419 (2004). [[http://www.bu.edu/abl/pdf/pnas_kobayashi.pdf pdf file]]
+
-
 
+
-
 
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Mason J, Linsay P, Collins JJ and Glass L. Evolving complex dynamics in electronic models of genetic networks. Chaos 14: 707-715 (2004). [[http://www.bu.edu/abl/pdf/chaos_mason.pdf pdf file]]
+
-
 
+
-
 
+
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Isaacs FJ, Hasty J, Cantor CR and Collins JJ. Prediction and measurement of an autoregulatory genetic module. Proceedings of the National Academy of Sciences USA 100: 7714-7719 (2003). [[http://www.bu.edu/abl/pdf/isaacs2003.pdf pdf file]]
+
-
 
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-
 
+
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Blake WJ, Kaern M, Cantor CR and Collins JJ. Noise in eukaryotic gene expression. Nature 422: 633-637 (2003). [[http://www.bu.edu/abl/pdf/blake2003.pdf?file=/nature/journal/v422/n6932/full/nature01546_fs.html&content_filetype=PDF pdf file]]
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-
 
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-
 
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Kaern M, Blake WJ and Collins JJ. The engineering of gene regulatory networks. Annual Review of Biomedical Engineering 5: 179-206 (2003). [[http://www.bu.edu/abl/pdf/kaern2003.pdf pdf file]]
+
-
 
+
-
 
+
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Hasty J, McMillen D and Collins JJ. Engineered gene circuits. Nature 420: 224-230 (2002).  [[http://www.bu.edu/abl/pdf/hasty2002.pdf?file=/nature/journal/v420/n6912/full/nature01257_fs.html&content_filetype=PDF pdf file]]
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-
 
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-
 
+
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Hasty J, Dolnik M, Rottschafer V and Collins JJ. A synthetic gene network for entraining and amplifying cellular oscillations. Physical Review Letters 88: 148101 (2002). [[http://www.bu.edu/abl/pdf/hasty2002prl.pdf?filetype=pdf&id=PRLTAO000088000014148101000001&idtype=cvips pdf file]]
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McMillen D, Kopell N, Hasty J and Collins JJ. Synchronizing genetic relaxation oscillators with intercell signaling. Proceedings of the National Academy of Sciences USA 99: 679-684 (2002). [[http://www.bu.edu/abl/pdf/mcmillen2002.pdf pdf file]]
+
-
 
+
-
 
+
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Hasty J and Collins JJ. Translating the noise. Nature Genetics 31: 13-14 (2002). [[http://www.bu.edu/abl/files/translating_the_noise.pdf pdf file]]
+
-
 
+
-
 
+
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Hasty J, McMillen D, Isaacs F and Collins JJ. Computational studies of gene regulatory networks: In numero molecular biology. Nature Reviews Genetics 2: 268-279 (2001). [[http://www.bu.edu/abl/pdf/hasty2001nature.pdf?file=/nrg/journal/v2/n4/full/nrg0401_268a_fs.html&filetype=PDF pdf file]]
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Hasty J, Isaacs F, Dolnik M, McMillen D and Collins JJ. Designer gene networks: Towards fundamental cellular control. CHAOS 11: 207-220 (2001). [[http://www.bu.edu/abl/pdf/hasty2001chaos.pdf pdf file]]
+
-
 
+
-
 
+
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Gardner TS and Collins JJ. Neutralizing noise in gene networks. Nature 405: 520-521 (2000). [[http://www.bu.edu/abl/files/neutralizing_noise_in.pdf pdf file]]
+
-
 
+
-
 
+
-
Hasty J, Pradines J, Dolnik M and Collins JJ. Noise-based switches and amplifiers for gene expression. Proceedings of the National Academy of Sciences USA 97: 2075-2080 (2000). [[http://www.bu.edu/abl/pdf/hasty2000pnas.pdf pdf file]]
+
-
 
+
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+
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Gardner TS, Cantor CR and Collins JJ. Construction of a genetic toggle switch in Escherichia coli. Nature 403: 339-342 (2000). [[http://www.bu.edu/abl/pdf/gardner2001nature.pdf?file=/nature/journal/v403/n6767/full/403339a0_fs.html&content_filetype=PDF pdf file]]
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'''Systems Biology'''
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Dwyer DJ, Kohanski MA, Hayete B, Collins JJ. Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli. Mol Syst Biol 3: 91 (2007). [[http://www.nature.com/msb/journal/v3/n1/pdf/msb4100135.pdf pdf file]]
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Ergun A, Lawrence CA, Kohanski MA, Brennan TA, Collins JJ. A network biology approach to prostate cancer. Mol Syst Biol 3: 82 (2007). [[http://www.nature.com/msb/journal/v3/n1/pdf/msb4100125.pdf pdf file]]
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Hayete B, Gardner TS, Collins JJ. Size matters: network inference tackles the genome scale. Mol Syst Biol 3: 77 (2007). [[http://www.nature.com/msb/journal/v3/n1/pdf/msb4100118.pdf pdf file]]
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Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S,
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Collins JJ, Gardner TS. Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles. PLoS Biol 9;5(1):e8 (2007). [[http://biology.plosjournals.org/archive/1545-7885/5/1/pdf/10.1371_journal.pbio.0050008-S.pdf pdf file]]
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di Bernardo D, Thompson MJ, Gardner TS, Chobot SE, Eastwood EL, Wojtovich AP, Elliot SJ, Schaus SE and Collins JJ. Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nature Biotechnology 23: 377-383 (2005). [[http://www.bu.edu/abl/files/nbt_dibernardo.pdf pdf file]]
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Gardner TS, Shimer S and Collins JJ. Inferring microbial genetic networks. ASM News 70: 121-126 (2004). [[http://www.bu.edu/abl/pdf/asm_gardner.pdf pdf file]]
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Gardner TS, Bernardo D, Lorenz D and Collins JJ. Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301: 102-105 (2003). [[http://www.bu.edu/abl/pdf/gardner2003.pdf pdf file]]
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Tegner J, Yeung MKS, Hasty J and Collins JJ. Reverse engineering gene networks - Integrating genetic perturbations with dynamical modeling. Proceedings of the National Academy of Sciences USA 100: 5944-5949 (2003). [[http://www.bu.edu/abl/pdf/tegner2003.pdf pdf file]]
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Yeung MKS, Tegner J and Collins JJ. Reverse engineering gene networks using singular value decomposition and robust regression. Proceedings of the National Academy of Sciences USA 99: 6163-6168 (2002). [[http://www.bu.edu/abl/pdf/yeung2002.pdf pdf file]]
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Hasty J and Collins JJ. Protein interactions: unspinning the web. Nature 411: 30-31 (2001). [[http://www.bu.edu/abl/files/unspinning_the_web.pdf pdf file]]
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Current revision

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  1. Brynildsen MP and Collins JJ. Systems biology makes it personal. Molecular Cell 34: 137-138 (2009). [1]
  2. Camacho DM and Collins JJ. Systems biology strikes gold. Cell 137: 24-26 (2009). [2]
  3. Schembri F, Sridhar S, Perdomo C, Gustafson AM, Zhang X, Ergun A, Lu J, Liu G, Zhang X, Bowers J, Vaziri C, Ott K, Sensinger K, Collins JJ, Brody JS, Getts R, Lenburg ME and Spira A. MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium. Proceedings of the National Academy of Sciences USA 106: 2319-2324 (2009). [3]
  4. Lorenz DR, Cantor CR and Collins JJ. A network biology approach to aging in yeast. Proceedings of the National Academy of Sciences USA 106: 1145-1150 (2009). [4]
  5. Dwyer DJ, Kohanski MA and Collins JJ. Networking opportunities for bacteria. Cell 135: 1153-1156 (2008). [5]
  6. Kohanski MA, Dwyer DJ, Wierzbowski J, Cottarel G and Collins JJ. Mistranslation of membrane proteins and two-component system activation trigger antibiotic-mediated cell death. Cell 135: 679-690 (2008). [6]
  7. Heng TS, Painter MW, Elpek K, Lukacs-Kornek V, Mauermann N, Turley SJ, Koller D, Kim FS, Wagers AJ, Asinovski N, Davis S, Fassett M, Feuerer M, Gray DH, Haxhinasto S, Hill JA, Hyatt G, Laplace C, Leatherbee K, Mathis D, Benoist C, Jianu R, Laidlaw DH, Best JA, Knell J, Goldrath AW, Jarjoura J, Sun JC, Zhu Y, Lanier LL, Ergun A, Li Z, Collins JJ, Shinton SA, Hardy RR, Friedline R, Sylvia K and Kang J. The Immunological Genome Project: networks of gene expression in immune cells.  Nature Immunolology 9: 1091-1094 (2008). [7]
  8. Ellis T, Wang X and Collins JJ. Gene regulation: hacking the network on a sugar high. Molecular Cell 30: 1-2 (2008). [8]
  9. Kohanski MA, Dwyer DJ, Hayete B, Lawrence CA and Collins JJ. A common mechanism of cellular death induced by bactericidal antibiotics. Cell 130: 797-810 (2007). [9]
  10. Dwyer DJ, Kohanski MA, Hayete B and Collins JJ. Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli. Molecular Systems Biology 3: 91 (2007). [10]
  11. Ergun A, Lawrence CA, Kohanski MA, Brennan TA and Collins JJ. A network biology approach to prostate cancer. Molecular Systems Biology 3: 82 (2007). [11]
  12. Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ and Gardner TS. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biology 5(1): e8 (2007). [12]
  13. Hayete B, Gardner TS and Collins JJ. Size matters: network inference tackles the genome scale. Molecular Systems Biology 3: 77 (2007). [13]
  14. di Bernardo D, Thompson MJ, Gardner TS, Chobot SE, Eastwood EL, Wojtovich AP, Elliot SJ, Schaus SE and Collins JJ. Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nature Biotechnology 23: 377-383 (2005). [14]
  15. Gardner TS, Shimer S and Collins JJ. Inferring microbial genetic networks. ASM News 70: 121-126 (2004). [15]
  16. Gardner TS, Bernardo D, Lorenz D and Collins JJ. Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301: 102-105 (2003). [16]
  17. Tegner J, Yeung MKS, Hasty J and Collins JJ. Reverse engineering gene networks - Integrating genetic perturbations with dynamical modeling. Proceedings of the National Academy of Sciences USA 100: 5944-5949 (2003). [17]
  18. Yeung MKS, Tegner J and Collins JJ. Reverse engineering gene networks using singular value decomposition and robust regression. Proceedings of the National Academy of Sciences USA 99: 6163-6168 (2002). [18]
  19. Hasty J and Collins JJ. Protein interactions: unspinning the web. Nature 411: 30-31 (2001). [19]


SYNTHETIC BIOLOGY

  1. Friedland AE, Lu TK, Wang X, Shi D, Church G and Collins JJ. Synthetic gene networks that count. Science 324: 1199-1202 (2009). [20]
  2. Ellis T, Wang X and Collins JJ. Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nature Biotechnology 27: 465-471 (2009). [21]
  3. Lu TK and Collins JJ. Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy. Proceedings of the National Academy of Sciences USA 106: 4629-4634 (2009). [22]
  4. Kohanski MA and Collins JJ. Rewiring bacteria, two components at a time. Cell 133: 947-948 (2008). [23]
  5. Guido NJ, Lee P, Wang X, Elston TC and Collins JJ. A pathway and genetic factors contributing to elevated gene expression noise in stationary phase. Biophysical Journal 93: L55-L57 (2007). [24]
  6. Deans TL, Cantor CR and Collins JJ. A tunable genetic switch based on RNAi and repressor proteins for regulating gene expression in mammalian cells. Cell 130: 363-372 (2007). [25]
  7. Murphy KF, Balazsi G and Collins JJ. Combinatorial promoter design for engineering noisy gene expression. Proceedings of the National Academy of Sciences USA 104: 12726-12731 (2007). [26]
  8. Lu TK and Collins JJ. Dispersing biofilms with engineered enzymatic bacteriophage. Proceedings of the National Academy of Sciences USA 104: 11197-11202 (2007). [27]
  9. Balazsi G and Collins JJ. Taking the inventory inside single cells. Nature Chemical Biology 3: 141-142 (2007). [28]
  10. Blake WJ, Balazsi G, Kohanski MA, Isaacs FJ, Murphy KF, Kuang Y, Cantor CR, Collins JJ. Phenotypic consequences of promoter-mediated transcriptional noise. Molecular Cell 24: 853-865 (2006). [29]
  11. Baker D, Church G, Collins J, Endy D, Jacobson J, Keasling J, Modrich P, Smolke C, Weiss R. Engineering life: building a FAB for biology. Scientific American 294: 44-51 (2006). [30]
  12. Isaacs FJ, Dwyer DJ and Collins JJ. RNA synthetic biology. Nature Biotechnology 24: 545-554 (2006). [31]
  13. Guido NJ, Wang X, Adalsteinsson D, McMillen D, Hasty J, Cantor CR, Elston TC and Collins JJ. A bottom-up approach to gene regulation. Nature 439: 856-860 (2006). [32]
  14. Blake WJ and Collins JJ. And the noise played on: stochastic gene expression and HIV-1 infection. Cell 122: 147-155 (2005). [33]
  15. Kaern M, Elston TC, Blake WJ, and Collins JJ. Stochasticity in gene expression: from theories to phenotypes. Nature Reviews Genetics 6: 451-464 (2005). [34]
  16. Isaacs FJ, Blake WJ and Collins JJ. Signal processing in single cells. Science 307: 1886-1888 (2005). [35]
  17. Isaacs FJ and Collins JJ. Plug-and-play with RNA. Nature Biotechnology 23: 306-307 (2005). [36]
  18. Isaacs FJ, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR and Collins JJ. Engineered riboregulators enable post-transcriptional control of gene expression. Nature Biotechnology 22: 841-847 (2004). [37]
  19. Kobayashi H, Kaern M, Araki M, Chung K, Gardner TS, Cantor CR and Collins JJ. Programmable cells: Interfacing natural and engineered gene networks. Proceedings of the National Academy of Sciences USA 101: 8414-8419 (2004). [38]
  20. Mason J, Linsay P, Collins JJ and Glass L. Evolving complex dynamics in electronic models of genetic networks. Chaos 14: 707-715 (2004). [39]
  21. Isaacs FJ, Hasty J, Cantor CR and Collins JJ. Prediction and measurement of an autoregulatory genetic module. Proceedings of the National Academy of Sciences USA 100: 7714-7719 (2003). [40]
  22. Blake WJ, Kaern M, Cantor CR and Collins JJ. Noise in eukaryotic gene expression. Nature 422: 633-637 (2003). [41]
  23. Kaern M, Blake WJ and Collins JJ. The engineering of gene regulatory networks. Annual Review of Biomedical Engineering 5: 179-206 (2003). [42]
  24. Hasty J, McMillen D and Collins JJ. Engineered gene circuits. Nature 420: 224-230 (2002). [43]
  25. Hasty J, Dolnik M, Rottschafer V and Collins JJ. A synthetic gene network for entraining and amplifying cellular oscillations. Physical Review Letters 88: 148101 (2002). [44]
  26. McMillen D, Kopell N, Hasty J and Collins JJ. Synchronizing genetic relaxation oscillators with intercell signaling. Proceedings of the National Academy of Sciences USA 99: 679-684 (2002). [45]
  27. Hasty J and Collins JJ. Translating the noise. Nature Genetics 31: 13-14 (2002). [46]
  28. Hasty J, McMillen D, Isaacs F and Collins JJ. Computational studies of gene regulatory networks: In numero molecular biology. Nature Reviews Genetics 2: 268-279 (2001). [47]
  29. Hasty J, Isaacs F, Dolnik M, McMillen D and Collins JJ. Designer gene networks: Towards fundamental cellular control. CHAOS 11: 207-220 (2001). [48]
  30. Gardner TS and Collins JJ. Neutralizing noise in gene networks. Nature 405: 520-521 (2000). [49]
  31. Hasty J, Pradines J, Dolnik M and Collins JJ. Noise-based switches and amplifiers for gene expression. Proceedings of the National Academy of Sciences USA 97: 2075-2080 (2000). [50]
  32. Gardner TS, Cantor CR and Collins JJ. Construction of a genetic toggle switch in Escherichia coli. Nature 403: 339-342 (2000). [51]


NOISE-ENHANCED SENSORIMOTOR FUNCTION

  1. Priplata AA, Patritti BL, Niemi JB, Hughes R, Gravelle DC, Lipsitz LA, Veves A, Stein J, Bonato P and Collins JJ. Noise-enhanced balance control in patients with diabetes and patients with stroke. Annals of Neurology 59: 4-12 (2006). [52]
  2. Harry JD, Niemi JB, Priplata AA and Collins JJ. Balancing act. IEEE Spectrum, April: 36-41 (2005). [53]
    ieeespectrum_harry.pdf]
  3. Priplata AA, Niemi JB, Harry JD, Lipsitz LA and Collins JJ. Vibrating insoles and balance control in elderly people. The Lancet 362: 1123-1124 (2003). [54]
  4. Collins JJ, Priplata AA, Gravelle DC, Niemi J, Harry J and Lipsitz LA. Noise-enhanced human sensorimotor function. IEEE Engineering in Medicine and Biology Magazine 22: 76-83 (2003). [55]
  5. Priplata AA, Niemi J, Salen M, Harry J, Lipsitz LA and Collins JJ. Noise-enhanced human balance control. Physical Review Letters 89: 238101 (2002). [56]
  6. Gravelle DC, Laughton CA, Dhruv NT, Katdare KD, Niemi JB, Lipsitz LA and Collins JJ. Noise-enhanced balance control in older adults. Neuroreport 13: 1853-1856 (2002). [57]
  7. Dhruv NT, Niemi JB, Harry JD, Lipsitz LA and Collins JJ. Enhancing tactile sensation in older adults with electrical noise stimulation. Neuroreport 13: 597-600 (2002). [58]
  8. Liu W, Lipsitz LA, Montero-Odasso M, Bean J, Kerrigan DC and Collins JJ. Noise-enhanced vibrotactile sensitivity in older adults and patients with stroke and patients with diabetic neuropathy. Archives of Physical Medicine and Rehabilitation 83: 171-176 (2002). [59]
  9. Nozaki D, Collins JJ and Yamamoto Y. Mechanism of stochastic resonance enhancement in neuronal models driven by 1/f noise. Physical Review E 60: 4637-4644 (1999). [60]
  10. Pradines JR, Osipov GV and Collins JJ. Coherence resonance in excitable and oscillatory systems: the essential role of slow and fast dynamics.  Physical Review E 60: 6407-6410 (1999). [61]
  11. Neiman A, Schimansky-Geier L, Moss F, Shulgin B and Collins JJ. Synchronization of noisy systems by stochastic signals. Physical Review E 60: 284-292 (1999). [62]
  12. Nozaki D, Mar DJ, Grigg P and Collins JJ. Effects of colored noise on stochastic resonance in sensory neurons. Physical Review Letters 82: 2402-2405 (1999). [63]
  13. Collins JJ. Fishing for function in noise. Nature 402: 241-242 (1999). [64]
  14. Suki B, Alencar AM, Sujeer MK, Lutchen KR, Collins JJ, Andrade JS, Ingenito EP, Zapperi S and Stanley HE. Life-support system benefits from noise. Nature 393: 127-128 (1998). [65]
  15. Richardson KA, Imhoff TT, Grigg P and Collins JJ. Using electrical noise to enhance the ability of humans to detect subthreshold mechanical cutaneous stimuli. CHAOS 8: 599-603 (1998). [66]
  16. Chow CC, Imhoff TT and Collins JJ. Enhancing aperiodic stochastic resonance through noise modulation. CHAOS 8: 616-620 (1998). [67]
  17. Gailey PC, Neiman A, Collins JJ and Moss F. Stochastic resonance in ensembles of nondynamical elements: the role of internal noise. Physical Review Letters 79: 4701-4704 (1997). [68]
  18. Collins JJ, Imhoff TT and Grigg P. Noise-mediated enhancements and decrements in human tactile sensation. Physical Review E 56: 923-926 (1997). [69]
  19. Cordo P, Inglis JT, Verschueren S, Collins JJ, Merfeld DM, Rosenblum S, Buckley S and Moss F. Noise in human muscle spindles. Nature 383: 769-770 (1996). [70]
  20. Collins JJ, Imhoff TT and Grigg P. Noise-enhanced tactile sensation. Nature 383: 770 (1996). [71]
  21. Collins JJ, Imhoff TT and Grigg P. Noise-enhanced information transmission in rat SA1 cutaneous mechanoreceptors via aperiodic stochastic resonance. Journal of Neurophysiology 76: 642-645 (1996). [72]
  22. Collins JJ, Chow CC, Capela AC and Imhoff TT. Aperiodic stochastic resonance. Physical Review E 54: 5575-5584 (1996). [73]
  23. Heneghan C, Chow CC, Collins JJ, Imhoff TT, Lowen SB and Teich MC. Information measures quantifying aperiodic stochastic resonance. Physical Review E 54: R2228-R2231 (1996). [74]
  24. Collins JJ, Chow CC and Imhoff TT. Aperiodic stochastic resonance in excitable systems. Physical Review E 52: R3321-R3324 (1995). [75]
  25. Collins JJ, Chow CC and Imhoff TT. Stochastic resonance without tuning. Nature 376: 236-238 (1995). [76]
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