Collins Lab:Reprints: Difference between revisions
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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 | 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]] | ||
Isaacs FJ, Dwyer DJ and Collins JJ. RNA synthetic biology. Nature Biotechnology 24: 545-554 (2006). | 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]] | ||
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). | 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]] | ||
Blake WJ and Collins JJ. And the noise played on: stochastic gene expression and HIV-1 infection. Cell 122: 147-155 (2005). | 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]] | ||
Kaern M, Elston TC, Blake WJ, and Collins JJ. Stochasticity in gene expression: from theories to phenotypes. Nature Reviews Genetics 6: 451-464 (2005). | 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]] | ||
Isaacs FJ, Blake WJ and Collins JJ. Signal processing in single cells. Science 307: 1886-1888 (2005). | 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]] | ||
Isaacs FJ and Collins JJ. Plug-and-play with RNA. Nature Biotechnology 23: 306-307 (2005). | 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]] | ||
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). | 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]] | ||
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). | 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]] | ||
Mason J, Linsay P, Collins JJ and Glass L. Evolving complex dynamics in electronic models of genetic networks. Chaos 14: 707-715 (2004). | 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]] | ||
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). | 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]] | ||
Blake WJ, Kaern M, Cantor CR and Collins JJ. Noise in eukaryotic gene expression. Nature 422: 633-637 (2003). | 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]] | ||
Kaern M, Blake WJ and Collins JJ. The engineering of gene regulatory networks. Annual Review of Biomedical Engineering 5: 179-206 (2003). | 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]] | ||
Hasty J, McMillen D and Collins JJ. Engineered gene circuits. Nature 420: 224-230 (2002). | 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]] | ||
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). | 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]] | ||
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). | 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]] | ||
Hasty J and Collins JJ. Translating the noise. Nature Genetics 31: 13-14 (2002). | 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]] | ||
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). | 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]] | ||
Hasty J, Isaacs F, Dolnik M, McMillen D and Collins JJ. Designer gene networks: Towards fundamental cellular control. CHAOS 11: 207-220 (2001). | 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]] | ||
Gardner TS and Collins JJ. Neutralizing noise in gene networks. Nature 405: 520-521 (2000). | 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). | 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]] | ||
Gardner TS, Cantor CR and Collins JJ. Construction of a genetic toggle switch in Escherichia coli. Nature 403: 339-342 (2000). | 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]] | ||
'''Systems Biology''' | '''Systems Biology''' | ||
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). | 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]] | ||
Gardner TS, Shimer S and Collins JJ. Inferring microbial genetic networks. ASM News 70: 121-126 (2004). | 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]] | ||
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). | 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]] | ||
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). | 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]] | ||
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). | 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]] | ||
Hasty J and Collins JJ. Protein interactions: unspinning the web. Nature 411: 30-31 (2001). | 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]] |
Revision as of 15:01, 29 December 2006
Synthetic Biology
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).
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). [pdf file]
Isaacs FJ, Dwyer DJ and Collins JJ. RNA synthetic biology. Nature Biotechnology 24: 545-554 (2006). [pdf file]
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). [pdf file]
Blake WJ and Collins JJ. And the noise played on: stochastic gene expression and HIV-1 infection. Cell 122: 147-155 (2005). [pdf file]
Kaern M, Elston TC, Blake WJ, and Collins JJ. Stochasticity in gene expression: from theories to phenotypes. Nature Reviews Genetics 6: 451-464 (2005). [pdf file]
Isaacs FJ, Blake WJ and Collins JJ. Signal processing in single cells. Science 307: 1886-1888 (2005). [pdf file]
Isaacs FJ and Collins JJ. Plug-and-play with RNA. Nature Biotechnology 23: 306-307 (2005). [pdf file]
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). [pdf file]
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). [pdf file]
Mason J, Linsay P, Collins JJ and Glass L. Evolving complex dynamics in electronic models of genetic networks. Chaos 14: 707-715 (2004). [pdf file]
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). [pdf file]
Blake WJ, Kaern M, Cantor CR and Collins JJ. Noise in eukaryotic gene expression. Nature 422: 633-637 (2003). [pdf file]
Kaern M, Blake WJ and Collins JJ. The engineering of gene regulatory networks. Annual Review of Biomedical Engineering 5: 179-206 (2003). [pdf file]
Hasty J, McMillen D and Collins JJ. Engineered gene circuits. Nature 420: 224-230 (2002). [pdf file]
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). [pdf file]
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). [pdf file]
Hasty J and Collins JJ. Translating the noise. Nature Genetics 31: 13-14 (2002). [pdf file]
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). [pdf file]
Hasty J, Isaacs F, Dolnik M, McMillen D and Collins JJ. Designer gene networks: Towards fundamental cellular control. CHAOS 11: 207-220 (2001). [pdf file]
Gardner TS and Collins JJ. Neutralizing noise in gene networks. Nature 405: 520-521 (2000). [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). [pdf file]
Gardner TS, Cantor CR and Collins JJ. Construction of a genetic toggle switch in Escherichia coli. Nature 403: 339-342 (2000). [pdf file]
Systems Biology
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). [pdf file]
Gardner TS, Shimer S and Collins JJ. Inferring microbial genetic networks. ASM News 70: 121-126 (2004). [pdf file]
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). [pdf file]
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). [pdf file]
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). [pdf file]
Hasty J and Collins JJ. Protein interactions: unspinning the web. Nature 411: 30-31 (2001). [pdf file]