U Alon

Summary

Affiliation: Weizmann Institute of Science
Country: Israel

Publications

  1. ncbi request reprint Network motifs: theory and experimental approaches
    Uri Alon
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Nat Rev Genet 8:450-61. 2007
  2. doi request reprint Defined order of evolutionary adaptations: experimental evidence
    Erez Oxman
    Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
    Evolution 62:1547-54. 2008
  3. pmc A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli
    Shiraz Kalir
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
    Mol Syst Biol 1:2005.0006. 2005
  4. pmc An analytically solvable model for rapid evolution of modular structure
    Nadav Kashtan
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
    PLoS Comput Biol 5:e1000355. 2009
  5. pmc Oscillations and variability in the p53 system
    Naama Geva-Zatorsky
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
    Mol Syst Biol 2:2006.0033. 2006
  6. pmc Extinctions in heterogeneous environments and the evolution of modularity
    Nadav Kashtan
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
    Evolution 63:1964-75. 2009
  7. pmc Facilitated variation: how evolution learns from past environments to generalize to new environments
    Merav Parter
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
    PLoS Comput Biol 4:e1000206. 2008
  8. pmc Dynamic proteomics of human protein level and localization across the cell cycle
    Shlomit Farkash-Amar
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
    PLoS ONE 7:e48722. 2012
  9. pmc Noise genetics: inferring protein function by correlating phenotype with protein levels and localization in individual human cells
    Shlomit Farkash-Amar
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
    PLoS Genet 10:e1004176. 2014
  10. pmc Evolutionary tradeoffs between economy and effectiveness in biological homeostasis systems
    Pablo Székely
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
    PLoS Comput Biol 9:e1003163. 2013

Collaborators

Detail Information

Publications67

  1. ncbi request reprint Network motifs: theory and experimental approaches
    Uri Alon
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Nat Rev Genet 8:450-61. 2007
    ..Here I review network motifs and their functions, with an emphasis on experimental studies. Network motifs in other biological networks are also mentioned, including signalling and neuronal networks...
  2. doi request reprint Defined order of evolutionary adaptations: experimental evidence
    Erez Oxman
    Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
    Evolution 62:1547-54. 2008
    ..We experimentally find this order reversal under the predicted conditions. This study supports a view in which the evolutionary path to adaptation in a new environment can be captured by theory and experiment...
  3. pmc A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli
    Shiraz Kalir
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
    Mol Syst Biol 1:2005.0006. 2005
    ..The SUM-FFL in this system works as theoretically predicted despite being embedded in at least two additional feedback loops. The present function might be carried out by the SUM-FFL in systems found across organisms...
  4. pmc An analytically solvable model for rapid evolution of modular structure
    Nadav Kashtan
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
    PLoS Comput Biol 5:e1000355. 2009
    ..In particular, the model suggests a mechanism for the dramatic speedup in evolution observed under such temporally varying goals...
  5. pmc Oscillations and variability in the p53 system
    Naama Geva-Zatorsky
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
    Mol Syst Biol 2:2006.0033. 2006
    ..This study provides a view of the extensive variability of the behavior of a protein circuit in living human cells, both from cell to cell and in the same cell over time...
  6. pmc Extinctions in heterogeneous environments and the evolution of modularity
    Nadav Kashtan
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
    Evolution 63:1964-75. 2009
    ..This study suggests, therefore, that extinctions in heterogeneous environments promote the evolution of modular biological network structure, allowing local populations to effectively recombine their modules to recolonize niches...
  7. pmc Facilitated variation: how evolution learns from past environments to generalize to new environments
    Merav Parter
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
    PLoS Comput Biol 4:e1000206. 2008
    ..Thus, environments that change in a systematic, modular fashion seem to promote facilitated variation and allow evolution to generalize to novel conditions...
  8. pmc Dynamic proteomics of human protein level and localization across the cell cycle
    Shlomit Farkash-Amar
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
    PLoS ONE 7:e48722. 2012
    ..Most of the cell-cycle dependent proteins exhibit changes in cellular localization. Such changes can be a useful tool in the regulation of the cell-cycle being fast and efficient...
  9. pmc Noise genetics: inferring protein function by correlating phenotype with protein levels and localization in individual human cells
    Shlomit Farkash-Amar
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
    PLoS Genet 10:e1004176. 2014
    ..We recovered 30 known motility genes, and validated several novel ones by mild knockdown experiments. Noise genetics can complement standard genetics for a variety of phenotypes. ..
  10. pmc Evolutionary tradeoffs between economy and effectiveness in biological homeostasis systems
    Pablo Székely
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
    PLoS Comput Biol 9:e1003163. 2013
    ..We applied this approach to estimate parameters in three biological systems: response to heat shock and response to DNA damage in bacteria, and calcium homeostasis in mammals...
  11. pmc The mirror game as a paradigm for studying the dynamics of two people improvising motion together
    Lior Noy
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Proc Natl Acad Sci U S A 108:20947-52. 2011
    ..This is a step toward understanding the human ability to create novelty by improvising together...
  12. pmc Plasticity of the cis-regulatory input function of a gene
    Avraham E Mayo
    Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
    PLoS Biol 4:e45. 2006
    ..The input function that we studied thus appears to be plastic, in the sense that many of the mutations do not ruin the regulation completely but rather result in new ways to integrate the inputs...
  13. pmc Negative auto-regulation increases the input dynamic-range of the arabinose system of Escherichia coli
    Daniel Madar
    Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, 76100, Israel
    BMC Syst Biol 5:111. 2011
    ..To address this, we studied the negative auto-regulation motif in the arabinose utilization system of Escherichia coli, in which negative auto-regulation is part of a complex regulatory network...
  14. doi request reprint How to give a good talk
    Uri Alon
    Department Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel Correspondence
    Mol Cell 36:165-7. 2009
    ..Here, I describe how to prepare, present, and answer questions in a scientific talk. We will see how a talk prepared with a single premise and delivered with good eye contact is clear and enjoyable...
  15. ncbi request reprint Biological networks: the tinkerer as an engineer
    U Alon
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel 76100
    Science 301:1866-7. 2003
    ..This viewpoint comments on recent advances in understanding the design principles of biological networks. It highlights the surprising discovery of "good-engineering" principles in biochemical circuitry that evolved by random tinkering...
  16. doi request reprint How to choose a good scientific problem
    Uri Alon
    Department Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Mol Cell 35:726-8. 2009
    ..This lack of explicit discussion leaves a vacuum that can lead to approaches such as choosing problems that can give results that merit publication in valued journals, resulting in a job and tenure...
  17. doi request reprint How to build a motivated research group
    Uri Alon
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Mol Cell 37:151-2. 2010
    ..Motivated group members experience a full sense of choice: of doing what one wants. Such behavior shows high performance, is enjoyable, and enhances innovation. This essay describes principles of building a motivated research group...
  18. pmc Robust control of PEP formation rate in the carbon fixation pathway of C(4) plants by a bi-functional enzyme
    Yuval Hart
    Dept of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
    BMC Syst Biol 5:171. 2011
    ..We asked how PEP formation rate, a key step in the carbon fixation pathway, might work at a precise rate, regulated by light, despite fluctuations in substrate and enzyme levels constituting and regulating this process...
  19. ncbi request reprint The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli
    S Mangan
    Department of Molecular Cell Biology and Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
    J Mol Biol 356:1073-81. 2006
    ..Response acceleration may be performed by the incoherent feed-forward loop modules that are found in diverse systems from bacteria to humans...
  20. ncbi request reprint Topological generalizations of network motifs
    N Kashtan
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel 76100
    Phys Rev E Stat Nonlin Soft Matter Phys 70:031909. 2004
    ..Using mathematical modeling, we describe the information processing functions of the different motif generalizations in transcription, neuronal, and electronic networks...
  21. ncbi request reprint Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs
    N Kashtan
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Bioinformatics 20:1746-58. 2004
    ..AVAILABILITY: A software tool for estimating subgraph concentrations and detecting network motifs (mfinder 1.1) and further information is available at http://www.weizmann.ac.il/mcb/UriAlon/..
  22. ncbi request reprint Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria
    S Kalir
    Department of Molecular Cell Biology, Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
    Science 292:2080-3. 2001
    ..The observed temporal program of transcription was much more detailed than was previously thought and was associated with multiple steps of flagella assembly...
  23. pmc Structure and function of the feed-forward loop network motif
    S Mangan
    Departments of Molecular Cell Biology and Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
    Proc Natl Acad Sci U S A 100:11980-5. 2003
    ..Additional features, such as pulse generation and cooperativity, are discussed. This study defines the function of one of the most significant recurring circuit elements in transcription networks...
  24. ncbi request reprint The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks
    S Mangan
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    J Mol Biol 334:197-204. 2003
    ..This information-processing function may be performed by the feedforward loop regulation modules that are found in diverse systems from bacteria to humans...
  25. ncbi request reprint Dynamic proteomics of individual cancer cells in response to a drug
    A A Cohen
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Science 322:1511-6. 2008
    ..We identify proteins whose dynamics differ widely between cells, in a way that corresponds to the outcomes-cell death or survival. This opens the way to understanding molecular responses to drugs in individual cells...
  26. ncbi request reprint Cost-benefit theory and optimal design of gene regulation functions
    Tomer Kalisky
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Phys Biol 4:229-45. 2007
    ..The present cost-benefit theory can be used to understand the shape of other gene regulatory functions in terms of environment and noise constraints...
  27. ncbi request reprint Network motifs in the transcriptional regulation network of Escherichia coli
    Shai S Shen-Orr
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Nat Genet 31:64-8. 2002
    ..The motif structure also allows an easily interpretable view of the entire known transcriptional network of the organism. This approach may help define the basic computational elements of other biological networks...
  28. pmc Coding limits on the number of transcription factors
    Shalev Itzkovitz
    Dept Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    BMC Genomics 7:239. 2006
    ..The total number of transcription factors encoded in a genome increases with the number of genes in the genome. Here, we examined the number of transcription factors from each super-family in diverse organisms...
  29. pmc Robustness in glyoxylate bypass regulation
    Guy Shinar
    Department of Molecular Cell Biology and Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
    PLoS Comput Biol 5:e1000297. 2009
    ..Instead, we suggest a robust mechanism where both substrates bind the bifunctional enzyme to form a ternary complex...
  30. pmc Generation of double-labeled reporter cell lines for studying co-dynamics of endogenous proteins in individual human cells
    Irina Issaeva
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
    PLoS ONE 5:e13524. 2010
    ..Thus, our approach provides an efficient tool for studying dynamic relationship between components of systems of interest at a single-cell level...
  31. ncbi request reprint Negative autoregulation speeds the response times of transcription networks
    Nitzan Rosenfeld
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    J Mol Biol 323:785-93. 2002
    ..This agrees with an analytical solution of a mathematical model for negative autoregulation. This may help in understanding the function of negative autoregulation, which appears in over 40% of known transcription factors in E.coli...
  32. pmc Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells
    Milana Frenkel-Morgenstern
    Molecular Cell Biology Department, Bioinformatics Unit, Weizmann Institute of Science, Rehovot 76100, Israel
    Nucleic Acids Res 38:D508-12. 2010
    ..The raw movies may be useful as a benchmark for developing image analysis tools for individual-cell dynamic-proteomics. The database is available at http://www.dynamicproteomics.net/...
  33. ncbi request reprint Response delays and the structure of transcription networks
    Nitzan Rosenfeld
    Department of Molecular Cell Biology, Weizmann Institute of Science, 76100, Rehovot, Israel
    J Mol Biol 329:645-54. 2003
    ..This study highlights a fundamental difference between the architecture of sensory and developmental transcription networks...
  34. ncbi request reprint Gene regulation at the single-cell level
    Nitzan Rosenfeld
    Departments of Molecular Cell Biology and Physics of Complex Systems, Weizmann Institute of Science, Rehovot, 76100, Israel
    Science 307:1962-5. 2005
    ..Thus, biochemical parameters, noise, and slowly varying cellular states together determine the effective single-cell GRF. These results can form a basis for quantitative modeling of natural gene circuits and for design of synthetic ones...
  35. pmc Detailed map of a cis-regulatory input function
    Y Setty
    Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
    Proc Natl Acad Sci U S A 100:7702-7. 2003
    ..This possibility means that the wild-type region is selected to perform an elaborate computation in setting the transcription rate. The present approach can be generally used to map the input functions of other genes...
  36. pmc Diverse two-dimensional input functions control bacterial sugar genes
    Shai Kaplan
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Mol Cell 29:786-92. 2008
    ..This first broad survey of two-dimensional input functions can be extended to map the logic of gene regulation in other systems...
  37. pmc Rules for biological regulation based on error minimization
    Guy Shinar
    Molecular Cell Biology and Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
    Proc Natl Acad Sci U S A 103:3999-4004. 2006
    ..The error-minimization framework raises several experimentally testable hypotheses. It may also apply to other biological regulation systems, such as those involving protein-protein interactions...
  38. ncbi request reprint Environmental selection of the feed-forward loop circuit in gene-regulation networks
    Erez Dekel
    Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, 76100, Israel
    Phys Biol 2:81-8. 2005
    ..This approach can be generally used to study the evolutionary selection of other network motifs...
  39. doi request reprint Evolutionary trade-offs, Pareto optimality, and the geometry of phenotype space
    O Shoval
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
    Science 336:1157-60. 2012
    ..Tasks can be inferred from measured phenotypes based on the behavior of organisms nearest the archetypes...
  40. ncbi request reprint Network motifs: simple building blocks of complex networks
    R Milo
    Departments of Physics of Complex Systems and Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel 76100
    Science 298:824-7. 2002
    ..Motifs may thus define universal classes of networks. This approach may uncover the basic building blocks of most networks...
  41. pmc The incoherent feed-forward loop can generate non-monotonic input functions for genes
    Shai Kaplan
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
    Mol Syst Biol 4:203. 2008
    ..The present study thus experimentally demonstrates how upstream circuitry can affect gene input functions and how an I1-FFL functions within its natural context in the cell...
  42. ncbi request reprint Optimality and evolutionary tuning of the expression level of a protein
    Erez Dekel
    Department of Molecular Cell Biology and Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot 76100, Israel
    Nature 436:588-92. 2005
    ..Thus, protein expression from the lac operon seems to be a solution of a cost-benefit optimization problem, and can be rapidly tuned by evolution to function optimally in new environments...
  43. pmc Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics
    Michal Ronen
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Proc Natl Acad Sci U S A 99:10555-60. 2002
    ..This finding opens the possibility of assigning kinetic parameters to transcriptional networks on a genomic scale...
  44. doi request reprint Understanding hydrogen-bond patterns in proteins using network motifs
    Ofer Rahat
    Department of Biological Chemistry, Department of Molecular Cell Biology and Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Bioinformatics 25:2921-8. 2009
    ..This may be due to differences in the pair-wise energy functions used and the dynamic nature of these proteins...
  45. ncbi request reprint Superfamilies of evolved and designed networks
    Ron Milo
    Departments of Molecular Cell Biology, Physics of Complex Systems, and Computer Science, Weizmann Institute of Science, Rehovot 76100, Israel
    Science 303:1538-42. 2004
    ..Additional superfamilies include power grids, protein-structure networks and geometric networks, World Wide Web links and social networks, and word-adjacency networks from different languages...
  46. ncbi request reprint Generation of a fluorescently labeled endogenous protein library in living human cells
    Alex Sigal
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Nat Protoc 2:1515-27. 2007
    ....
  47. ncbi request reprint Using a quantitative blueprint to reprogram the dynamics of the flagella gene network
    Shiraz Kalir
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel 76100
    Cell 117:713-20. 2004
    ..The present approach can be used to define blueprints of other gene networks and to quantitatively reprogram their dynamics...
  48. ncbi request reprint Cost of unneeded proteins in E. coli is reduced after several generations in exponential growth
    Irit Shachrai
    Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
    Mol Cell 38:758-67. 2010
    ....
  49. ncbi request reprint Just-in-time transcription program in metabolic pathways
    Alon Zaslaver
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
    Nat Genet 36:486-91. 2004
    ..Our findings suggest that metabolic regulation networks are designed to generate precision promoter timing and activity programs that can be understood using the engineering principles of production pipelines...
  50. pmc Spontaneous evolution of modularity and network motifs
    Nadav Kashtan
    Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
    Proc Natl Acad Sci U S A 102:13773-8. 2005
    ..The present study may shed light on the evolutionary forces that promote structural simplicity in biological networks and offers ways to improve the evolutionary design of engineered systems...
  51. pmc A fluctuation method to quantify in vivo fluorescence data
    Nitzan Rosenfeld
    Department of Molecular Biology, Weizmann Institute of Science, Rehovot, Israel
    Biophys J 91:759-66. 2006
    ..Our technique should provide a quantitative internal calibration to systems biology studies of both synthetic and endogenous cellular networks...
  52. ncbi request reprint Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins
    Alex Sigal
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Nat Methods 3:525-31. 2006
    ..This approach to dynamic proteomics can aid in discovery and accurate quantification of the extensive regulation of protein concentration and localization in individual living cells...
  53. ncbi request reprint A comprehensive library of fluorescent transcriptional reporters for Escherichia coli
    Alon Zaslaver
    Department of Molecular Cell Biology, Weizmann Institute of Science, 76100, Israel
    Nat Methods 3:623-8. 2006
    ..coli, including putative internal promoters within previously known operons, such as the lac operon. This library can serve as a tool for accurate, high-resolution analysis of transcription networks in living E. coli cells...
  54. ncbi request reprint Optimal gene partition into operons correlates with gene functional order
    Alon Zaslaver
    Department of Molecular Cell Biology and Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
    Phys Biol 3:183-9. 2006
    ..Thus gene functional order may be inferred by analyzing the operon structure across different genomes...
  55. ncbi request reprint Variability and memory of protein levels in human cells
    Alex Sigal
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100 Israel
    Nature 444:643-6. 2006
    ..The persistent memory for protein levels that we found might underlie individuality in cell behaviour and could set a timescale needed for signals to affect fully every member of a cell population...
  56. ncbi request reprint A module of negative feedback regulators defines growth factor signaling
    Ido Amit
    Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel
    Nat Genet 39:503-12. 2007
    ..More generally, our study proposes a mechanistic description of the cellular response to growth factors by defining architectural motifs that underlie the function of signaling networks...
  57. ncbi request reprint Simplicity in biology
    Uri Alon
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Nature 446:497. 2007
  58. pmc Varying environments can speed up evolution
    Nadav Kashtan
    Deptartment of Molecular Cell Biology and Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
    Proc Natl Acad Sci U S A 104:13711-6. 2007
    ..This study suggests that varying environments might significantly contribute to the speed of natural evolution. In addition, it suggests a way to accelerate optimization algorithms and improve evolutionary approaches in engineering...
  59. pmc Accurate prediction of gene feedback circuit behavior from component properties
    Nitzan Rosenfeld
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
    Mol Syst Biol 3:143. 2007
    ..This demonstration that quantitative characterization of regulatory elements can predict the behavior of genetic circuits supports a fundamental requirement of synthetic biology...
  60. pmc Precise temporal modulation in the response of the SOS DNA repair network in individual bacteria
    Nir Friedman
    Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot, Israel
    PLoS Biol 3:e238. 2005
    ....
  61. ncbi request reprint Coarse-graining and self-dissimilarity of complex networks
    Shalev Itzkovitz
    Departments of Molecular Cell Biology and Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
    Phys Rev E Stat Nonlin Soft Matter Phys 71:016127. 2005
    ..The present approach may be used to simplify a variety of directed and nondirected, natural and designed networks...
  62. pmc The genetic code is nearly optimal for allowing additional information within protein-coding sequences
    Shalev Itzkovitz
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
    Genome Res 17:405-12. 2007
    ..Whereas many of the known regulatory codes reside in nontranslated regions of the genome, the present findings suggest that protein-coding regions can readily carry abundant additional information...
  63. pmc Fourier analysis and systems identification of the p53 feedback loop
    Naama Geva-Zatorsky
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Proc Natl Acad Sci U S A 107:13550-5. 2010
    ..It seems to be a useful way to find the in vivo design of circuits and may be applied to other systems by monitoring their power spectrum in individual cells...
  64. doi request reprint Protein dynamics in drug combinations: a linear superposition of individual-drug responses
    Naama Geva-Zatorsky
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Cell 140:643-51. 2010
    ..Our approach might eliminate the need to increase the number of experiments exponentially with the number of drugs and suggests that it might be possible to rationally control protein dynamics with specific drug combinations...
  65. pmc Input output robustness in simple bacterial signaling systems
    Guy Shinar
    Departments of Molecular Cell Biology and Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
    Proc Natl Acad Sci U S A 104:19931-5. 2007
    ..It explains how specific molecular details can work together to provide robustness. Moreover, it suggests an approach that can help identify a wide family of nonequilibrium mechanisms that potentially have robust input-output relations...
  66. doi request reprint Central carbon metabolism as a minimal biochemical walk between precursors for biomass and energy
    Elad Noor
    Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
    Mol Cell 39:809-20. 2010
    ..This suggests an optimality principle for the structure of central carbon metabolism. The present approach may be used to study other metabolic networks and to design new minimal pathways...
  67. pmc Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction
    Esti Yeger-Lotem
    Department of Molecular Genetics and Biotechnology, Faculty of Medicine, Hebrew University, Jerusalem 91120, Israel
    Proc Natl Acad Sci U S A 101:5934-9. 2004
    ..Virtually all four-protein motifs consisted of combinations of smaller motifs. This study presents a basic framework for detecting the building blocks of networks with multiple types of interactions...