TY - JOUR AU - Lee, T. I. AU - Rinaldi, N. J. AU - Robert, F. AU - Odom, D. T. AU - Bar-Joseph, Z. AU - Gerber, G. K. AU - Hannett, N. M. AU - Harbison, C. T. AU - Thompson, C. M. AU - Simon, I. AU - Zeitlinger, J. AU - Jennings, E. G. AU - Murray, H. L. AU - Gordon, D. B. AU - Ren, B. AU - Wyrick, J. J. AU - Tagne, J. B. AU - Volkert, T. L. AU - Fraenkel, E. AU - Gifford, D. K. AU - Young, R. A. PY - 2002 DA - 2002// TI - Transcriptional Regulatory Networks in Saccharomyces cerevisiae JO - Science VL - 298 UR - https://doi.org/10.1126/science.1075090 DO - 10.1126/science.1075090 ID - Lee2002 ER - TY - JOUR AU - Shen-Orr, S. S. AU - Milo, R. AU - Mangan, S. AU - Alon, U. PY - 2002 DA - 2002// TI - Network motifs in the transcriptional regulation network of Escherichia coli JO - Nature Genetics VL - 31 UR - https://doi.org/10.1038/ng881 DO - 10.1038/ng881 ID - Shen-Orr2002 ER - TY - BOOK AU - Alon, U. PY - 2007 DA - 2007// TI - An introduction to Systems Biology. Design principles of biological circuits PB - Computational Biology CY - USA ID - Alon2007 ER - TY - JOUR AU - Tyson, J. J. AU - Chen, K. C. AU - Novak, B. PY - 2003 DA - 2003// TI - Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell JO - Current Opinion in Cell Biology VL - 15 UR - https://doi.org/10.1016/S0955-0674(03)00017-6 DO - 10.1016/S0955-0674(03)00017-6 ID - Tyson2003 ER - TY - JOUR AU - Mangan, S. AU - Zaslaver, A. AU - Alon, U. PY - 2003 DA - 2003// TI - The Coherent Feedforward Loop Serves as a Sign-sensitive Delay Element in Transcription Networks JO - Journal of Molecular Biology VL - 334 UR - https://doi.org/10.1016/j.jmb.2003.09.049 DO - 10.1016/j.jmb.2003.09.049 ID - Mangan2003 ER - TY - CHAP AU - Kalir, S. AU - Mangan, S. AU - Alon, U. PY - 2005 DA - 2005// TI - A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli BT - Molecular Systems Biology ID - Kalir2005 ER - TY - JOUR AU - Mangan, S. AU - Itzkovitz, S. AU - Zaslaver, A. AU - Alon, U. PY - 2006 DA - 2006// TI - The Incoherent Feed-forward Loop Accelerates the Response-time of the gal System of Escherichia coli JO - Journal of Molecular Biology VL - 356 UR - https://doi.org/10.1016/j.jmb.2005.12.003 DO - 10.1016/j.jmb.2005.12.003 ID - Mangan2006 ER - TY - JOUR AU - Zaslaver, A. AU - Bren, A. AU - Ronen, M. AU - Itzkovitz, S. AU - Kikoin, I. AU - Shavit, S. AU - Liebermeister, W. AU - Surette, M. AU - Alon, U. PY - 2006 DA - 2006// TI - A comprehensive library of fluorescent transcriptional reporters for Escherichia coli JO - Nature Methods VL - 3 UR - https://doi.org/10.1038/nmeth895 DO - 10.1038/nmeth895 ID - Zaslaver2006 ER - TY - JOUR AU - Cohen, A. A. AU - Geva-Zatorsky, N. AU - Eden, E. AU - Frenkel-Morgenstern, M. AU - Issaeva, I. AU - Sigal, A. AU - Milo, R. AU - Cohen-Saidon, C. AU - Liron, Y. AU - Kam, Z. AU - Cohen, L. AU - Danon, T. AU - Perzov, N. AU - Alon, U. PY - 2008 DA - 2008// TI - Dynamic proteomics of individual cancer cells in response to a drug JO - Science VL - 322 UR - https://doi.org/10.1126/science.1160165 DO - 10.1126/science.1160165 ID - Cohen2008 ER - TY - CHAP AU - Segal, E. AU - Barash, Y. AU - Simon, I. AU - Friedman, N. AU - Koller, D. PY - 2002 DA - 2002// TI - From promoter sequence to expression: a probabilistic framework BT - Proceedings of the Sixth Annual International Conference on Computational Molecular Biology (RECOMB) ID - Segal2002 ER - TY - JOUR AU - Brazhnik, P. AU - de la Fuente, A. AU - Mendes, P. PY - 2002 DA - 2002// TI - Gene networks: how to put the function in genomics JO - TRENDS in Biotechnology VL - 20 UR - https://doi.org/10.1016/S0167-7799(02)02053-X DO - 10.1016/S0167-7799(02)02053-X ID - Brazhnik2002 ER - TY - JOUR AU - Cavalier, G. AU - Anastassiou, D. PY - 2005 DA - 2005// TI - Phenotype analysis using network motifs derived from changes in regulatory network dynamics JO - Proteins: Structure, Function and Bioinformatics VL - 60 UR - https://doi.org/10.1002/prot.20538 DO - 10.1002/prot.20538 ID - Cavalier2005 ER - TY - JOUR AU - Swameye, I. AU - Müller, T. G. AU - Timmer, J. AU - Sandra, O. AU - Klingmüller, U. PY - 2003 DA - 2003// TI - Identification of nucleocytoplasmic cycling as a remote sensor in cellular signaling by databased modeling JO - PNAS VL - 100 UR - https://doi.org/10.1073/pnas.0237333100 DO - 10.1073/pnas.0237333100 ID - Swameye2003 ER - TY - JOUR AU - Vyshemirsky, V. AU - Girolami, M. A. PY - 2008 DA - 2008// TI - Bayesian ranking of biochemical system models JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btm607 DO - 10.1093/bioinformatics/btm607 ID - Vyshemirsky2008 ER - TY - BOOK AU - Gelman, A. AU - Carlin, J. B. AU - Stern, H. S. AU - Rubin, D. B. PY - 2004 DA - 2004// TI - Bayesian data analysis PB - Hall/CRC Texts in Statistical Science CY - USA ID - Gelman2004 ER - TY - BOOK AU - Gilks, W. R. AU - Richardson, S. AU - Spiegelhalter, D. J. PY - 1996 DA - 1996// TI - Markov Chain Monte Carlo in Practice PB - Hall/CRC Interdisciplinary Statistics Series CY - USA ID - Gilks1996 ER - TY - JOUR AU - Gelfand, A. E. AU - Dey, D. K. PY - 1994 DA - 1994// TI - Bayesian model choice: asymptotic and exact calculations JO - Journal of the Royal Statistics Society Series B (Methodological) VL - 56 ID - Gelfand1994 ER - TY - JOUR AU - Miazhynskaia, T. AU - Dorffner, G. PY - 2006 DA - 2006// TI - A comparison of Bayesian model selection based on MCMC with an application to GARCH-type models JO - Statistical Papers VL - 47 UR - https://doi.org/10.1007/s00362-006-0305-z DO - 10.1007/s00362-006-0305-z ID - Miazhynskaia2006 ER - TY - JOUR AU - Spiegelhalter, D. J. AU - Best, N. G. AU - Carlin, B. P. AU - Linde, A. v. a. n. d. e. r. PY - 2002 DA - 2002// TI - Bayesian measures of model complexity and fit JO - Journal of the Royal Statistics Society Series B VL - 64 UR - https://doi.org/10.1111/1467-9868.00353 DO - 10.1111/1467-9868.00353 ID - Spiegelhalter2002 ER - TY - BOOK AU - Ripley, B. D. PY - 1996 DA - 1996// TI - Pattern Recognition and Neural Networks PB - Cambridge University Press CY - Cambridge UR - https://doi.org/10.1017/CBO9780511812651 DO - 10.1017/CBO9780511812651 ID - Ripley1996 ER - TY - JOUR AU - Kass, R. E. AU - Raftery, A. E. PY - 1995 DA - 1995// TI - Bayes Factors JO - Journal of the American Statistical Association VL - 90 UR - https://doi.org/10.1080/01621459.1995.10476572 DO - 10.1080/01621459.1995.10476572 ID - Kass1995 ER - TY - BOOK AU - Burnham, K. P. AU - Anderson, D. R. PY - 2002 DA - 2002// TI - Model Selection and Multimodel Inference: a Practical Information-Theoretic Approach PB - Springer-Verlag CY - New York ID - Burnham2002 ER - TY - JOUR AU - Bois, F. Y. AU - Maszle, D. R. PY - 1997 DA - 1997// TI - MCSim: A Monte Carlo Simulation Program JO - Journal of Statistical Software VL - 2 UR - https://doi.org/10.18637/jss.v002.i09 DO - 10.18637/jss.v002.i09 ID - Bois1997 ER - TY - STD TI - The R Project for Statistical Computing. http://www.R-project.org UR - http://www.R-project.org ID - ref24 ER - TY - JOUR AU - Ronen, M. AU - Rosenberg, R. AU - Shraiman, B. I. AU - Alon, U. PY - 2002 DA - 2002// TI - Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics JO - Proceedings of the National Academy of Sciences of the USA VL - 99 UR - https://doi.org/10.1073/pnas.152046799 DO - 10.1073/pnas.152046799 ID - Ronen2002 ER - TY - JOUR AU - Alon, U. PY - 2007 DA - 2007// TI - Network motifs: theory and experimental approaches JO - Nature Reviews Genetics VL - 8 UR - https://doi.org/10.1038/nrg2102 DO - 10.1038/nrg2102 ID - Alon2007 ER - TY - JOUR AU - Batchelor, E. AU - Loewer, A. AU - Lahav, G. PY - 2009 DA - 2009// TI - The ups and downs of p53: understanding protein dynamics in single cells JO - Nature Reviews Cancer VL - 9 UR - https://doi.org/10.1038/nrc2604 DO - 10.1038/nrc2604 ID - Batchelor2009 ER - TY - JOUR AU - Mangan, S. AU - Alon, U. PY - 2003 DA - 2003// TI - Structure and function of the feed-forward loop network motif JO - Proceedings of the National Academy of Sciences of the USA VL - 100 UR - https://doi.org/10.1073/pnas.2133841100 DO - 10.1073/pnas.2133841100 ID - Mangan2003 ER - TY - JOUR AU - Ma, H. W. AU - Kumar, B. AU - Ditges, U. AU - Gunzer, F. AU - Buer, J. AU - Zeng, A. P. PY - 2004 DA - 2004// TI - An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs JO - Nucleic Acids Research VL - 32 UR - https://doi.org/10.1093/nar/gkh1009 DO - 10.1093/nar/gkh1009 ID - Ma2004 ER - TY - JOUR AU - Kalir, S. AU - Alon, U. PY - 2004 DA - 2004// TI - Using a quantitative blueprint to reprogram the dynamics of the flagella gene network JO - Cell VL - 117 UR - https://doi.org/10.1016/j.cell.2004.05.010 DO - 10.1016/j.cell.2004.05.010 ID - Kalir2004 ER - TY - JOUR AU - Omlin, M. AU - Reichert, P. PY - 1999 DA - 1999// TI - A comparison of techniques for the estimation of model prediction uncertainty JO - Ecological Modelling VL - 115 UR - https://doi.org/10.1016/S0304-3800(98)00174-4 DO - 10.1016/S0304-3800(98)00174-4 ID - Omlin1999 ER -