Defined Order of Evolutionary Adaptations: Experimental Evidence (2008)
Erez Oxman, Uri Alon, Erez Dekel
Organisms often adapt to new conditions by means of beneficial mutations that become fixed in the population. Often, full adaptation requires several different mutations in the same cell, each of...
Understanding Hydrogen-Bond Patterns in Proteins using a Novel Statistical Model (2008)
Ofer Rahat, Uri Alon, Yaakov Levy, Gideon Schreiber
Proteins are built from basic structural elements and their systematic characterization is of interest. Searching for recurring patterns in protein contact maps, we found several network motifs,...
Environmental variability and modularity of bacterial metabolic networks (2007)
Parter, Merav, Kashtan, Nadav, Alon, Uri
Abstract Background Biological systems are often modular: they can be decomposed into nearly-independent structural units that perform specific functions. The evolutionary origin of modularity is a...
The immune-body cytokine network defines a social architecture of cell interactions (2006)
Frankenstein, Ziv, Alon, Uri, Cohen, Irun R
Abstract Background Three networks of intercellular communication can be associated with cytokine secretion; one limited to cells of the immune system (immune cells), one limited to parenchymal cells...
Coding limits on the number of transcription factors (2006)
Itzkovitz, Shalev, Tlusty, Tsvi, Alon, Uri
Abstract Background Transcription factor proteins bind specific DNA sequences to control the expression of genes. They contain DNA binding domains which belong to several super-families, each with a...
Plasticity of the cis-Regulatory Input Function of a Gene (2006)
Avraham E. Mayo, Yaakov Setty, Seagull Shavit, Alon Zaslaver, Uri Alon
A few point mutations in the lac operon of Escherichia coli are sufficient to change the nature of the transcriptional computation.
Plasticity of the cis-Regulatory Input Function of a Gene (2006)
Avraham E. Mayo, Yaakov Setty, Seagull Shavit, Alon Zaslaver, Uri Alon
The transcription rate of a gene is often controlled by several regulators that bind specific sites in the gene's cis-regulatory region. The combined effect of these regulators is described by a...
Nir Friedman, Shuki Vardi, Michal Ronen, Uri Alon, Joel Stavans
Oscillations in transcriptional activity in the network responsible for controlling DNA damage are monitored with GFP- promoter fusions in individual E. coli cells.
Nir Friedman, Shuki Vardi, Michal Ronen, Uri Alon, Joel Stavans
The SOS genetic network is responsible for the repair/bypass of DNA damage in bacterial cells. While the initial stages of the response have been well characterized, less is known about the dynamics...
Search for computational modules in the C. elegansbrain (2004)
Reigl, Markus, Alon, Uri, Chklovskii, Dmitri B
Abstract Background Does the C. elegans nervous system contain multi-neuron computational modules that perform stereotypical functions? We attempt to answer this question by searching for recurring...
Subgraphs and network motifs in geometric networks (2004)
Many real-world networks describe systems in which interactions decay with the distance between nodes. Examples include systems constrained in real space such as transportation and communication...
Coarse-Graining and Self-Dissimilarity of Complex Networks (2004)
Itzkovitz, Shalev, Levitt, Reuven, Kashtan, Nadav, Milo, Ron, Itzkovitz, Michael, Alon, Uri
Can complex engineered and biological networks be coarse-grained into smaller and more understandable versions in which each node represents an entire pattern in the original network? To address...
Smooth Phases, Roughening Transitions and Novel Exponents in One-dimensional Growth Models (1997)
Alon, Uri, Evans, Martin, Hinrichsen, Haye, Mukamel, David
A class of solid-on-solid growth models with short range interactions and sequential updates is studied. The models exhibit both smooth and rough phases in dimension d=1. Some of the features of the...
Gel-Electrophoresis and Diffusion of Ring-Shaped DNA (1997)
A model for the motion of ring-shaped DNA in a gel is introduced and studied by numerical simulations and a mean-field approximation. The ring motion is mediated by finger-shaped loops (hernias) that...
Roughening Transition in a One-Dimensional Growth Process (1995)
Alon, Uri, Evans, Martin, Hinrichsen, Haye, Mukamel, David
A class of nonequilibrium models with short-range interactions and sequential updates is presented. The models describe one dimensional growth processes which display a roughening transition between...
Generation of oscillations by the p53-Mdm2 feedback loop: A theoretical and experimental study
Maya, Ruth, Segel, Lee A., Alon, Uri, Levine, Arnold J., Oren, Moshe
The intracellular activity of the p53 tumor suppressor protein is regulated through a feedback loop involving its transcriptional target, mdm2. We present a simple mathematical model suggesting that,...
Ronen, Michal, Rosenberg, Revital, Shraiman, Boris I., Alon, Uri
A basic challenge in systems biology is to understand the dynamical behavior of gene regulation networks. Current approaches aim at determining the network structure based on genomic-scale data....
Yeger-Lotem, Esti, Sattath, Shmuel, Kashtan, Nadav, Itzkovitz, Shalev, Milo, Ron, Pinter, Ron Y., ...
Genes and proteins generate molecular circuitry that enables the cell to process information and respond to stimuli. A major challenge is to identify characteristic patterns in this network of...
Spontaneous evolution of modularity and network motifs
Biological networks have an inherent simplicity: they are modular with a design that can be separated into units that perform almost independently. Furthermore, they show reuse of recurring patterns...
Precise Temporal Modulation in the Response of the SOS DNA Repair Network in Individual Bacteria
Friedman, Nir, Vardi, Shuki, Ronen, Michal, Alon, Uri, Stavans, Joel
The SOS genetic network is responsible for the repair/bypass of DNA damage in bacterial cells. While the initial stages of the response have been well characterized, less is known about the dynamics...
Plasticity of the cis-Regulatory Input Function of a Gene
Mayo, Avraham E, Setty, Yaakov, Shavit, Seagull, Zaslaver, Alon, Alon, Uri
The transcription rate of a gene is often controlled by several regulators that bind specific sites in the gene's cis-regulatory region. The combined effect of these regulators is described by a...
Rules for biological regulation based on error minimization
Shinar, Guy, Dekel, Erez, Tlusty, Tsvi, Alon, Uri
The control of gene expression involves complex mechanisms that show large variation in design. For example, genes can be turned on either by the binding of an activator (positive control) or the...
Generation of oscillations by the p53-Mdm2 feedback loop: A theoretical and experimental study
Maya, Ruth, Segel, Lee A., Alon, Uri, Levine, Arnold J., Oren, Moshe
The intracellular activity of the p53 tumor suppressor protein is regulated through a feedback loop involving its transcriptional target, mdm2. We present a simple mathematical model suggesting that,...
Ronen, Michal, Rosenberg, Revital, Shraiman, Boris I., Alon, Uri
A basic challenge in systems biology is to understand the dynamical behavior of gene regulation networks. Current approaches aim at determining the network structure based on genomic-scale data....
Yeger-Lotem, Esti, Sattath, Shmuel, Kashtan, Nadav, Itzkovitz, Shalev, Milo, Ron, Pinter, Ron Y., ...
Genes and proteins generate molecular circuitry that enables the cell to process information and respond to stimuli. A major challenge is to identify characteristic patterns in this network of...
Precise Temporal Modulation in the Response of the SOS DNA Repair Network in Individual Bacteria
Friedman, Nir, Vardi, Shuki, Ronen, Michal, Alon, Uri, Stavans, Joel
The SOS genetic network is responsible for the repair/bypass of DNA damage in bacterial cells. While the initial stages of the response have been well characterized, less is known about the dynamics...
Spontaneous evolution of modularity and network motifs
Biological networks have an inherent simplicity: they are modular with a design that can be separated into units that perform almost independently. Furthermore, they show reuse of recurring patterns...
Rules for biological regulation based on error minimization
Shinar, Guy, Dekel, Erez, Tlusty, Tsvi, Alon, Uri
The control of gene expression involves complex mechanisms that show large variation in design. For example, genes can be turned on either by the binding of an activator (positive control) or the...
Plasticity of the cis-Regulatory Input Function of a Gene
Mayo, Avraham E, Setty, Yaakov, Shavit, Seagull, Zaslaver, Alon, Alon, Uri
The transcription rate of a gene is often controlled by several regulators that bind specific sites in the gene's cis-regulatory region. The combined effect of these regulators is described by a...
Kalir, Shiraz, Mangan, Shmoolik, Alon, Uri
Complex gene-regulation networks are made of simple recurring gene circuits called network motifs. The functions of several network motifs have recently been studied experimentally, including the...
Oscillations and variability in the p53 system
Geva-Zatorsky, Naama, Rosenfeld, Nitzan, Itzkovitz, Shalev, Milo, Ron, Sigal, Alex, Dekel, Erez, ...
Understanding the dynamics and variability of protein circuitry requires accurate measurements in living cells as well as theoretical models. To address this, we employed one of the best-studied...
A Fluctuation Method to Quantify In Vivo Fluorescence Data
Rosenfeld, Nitzan, Perkins, Theodore J., Alon, Uri, Elowitz, Michael B., Swain, Peter S.
Quantitative in vivo measurements are essential for developing a predictive understanding of cellular behavior. Here we present a technique that converts observed fluorescence intensities into...
DNA sequences that code for proteins need to convey, in addition to the protein-coding information, several different signals at the same time. These “parallel codes” include binding sequences...
Accurate prediction of gene feedback circuit behavior from component properties
Rosenfeld, Nitzan, Young, Jonathan W, Alon, Uri, Swain, Peter S, Elowitz, Michael B
A basic assumption underlying synthetic biology is that analysis of genetic circuit elements, such as regulatory proteins and promoters, can be used to understand and predict the behavior of circuits...
Varying environments can speed up evolution
Kashtan, Nadav, Noor, Elad, Alon, Uri
Simulations of biological evolution, in which computers are used to evolve systems toward a goal, often require many generations to achieve even simple goals. It is therefore of interest to look for...
Input–output robustness in simple bacterial signaling systems
Shinar, Guy, Milo, Ron, Martínez, María Rodríguez, Alon, Uri
Biological signaling systems produce an output, such as the level of a phosphorylated protein, in response to defined input signals. The output level as a function of the input level is called the...
The incoherent feed-forward loop can generate non-monotonic input functions for genes
Kaplan, Shai, Bren, Anat, Dekel, Erez, Alon, Uri
Gene regulation networks contain recurring circuit patterns called network motifs. One of the most common network motif is the incoherent type 1 feed-forward loop (I1-FFL), in which an activator...
RECURRING HARMONIC WALKS AND NETWORK MOTIFS IN WESTERN MUSIC
SHALEV ITZKOVITZ, RON MILO, NADAV KASHTAN, REUVEN LEVITT, AMIR LAHAV, URI ALON
Western harmony is comprised of sequences of chords, which obey grammatical rules. It is of interest to develop a compact representation of the harmonic movement of chord sequences. Here, we apply an...
Facilitated Variation: How Evolution Learns from Past Environments To Generalize to New Environments
Parter, Merav, Kashtan, Nadav, Alon, Uri
One of the striking features of evolution is the appearance of novel structures in organisms. Recently, Kirschner and Gerhart have integrated discoveries in evolution, genetics, and developmental...