49 citations · 78 across the 12 of their papers we have counts for
16 papers
On the Exponent of Several Classes of Oscillatory Matrices
Yoram Zarai, Michael Margaliot
Oscillatory matrices were introduced in the seminal work of Gantmacher and Krein. An matrix is called oscillatory if all its minors are nonnegative and there exists…
Networks of ribosome flow models for modeling and analyzing intracellular traffic
Itzik Nanikashvili, Yoram Zarai, Alexander Ovseevich +2
The ribosome flow model with input and output (RFMIO) is a deterministic dynamical system that has been used to study the flow of ribosomes during mRNA translation. The RFMIO and i…
Dynamical Systems with a Cyclic Sign Variation Diminishing Property
Tsuff Ben-Avraham, Guy Sharon, Yoram Zarai +1
Several studies analyzed certain nonlinear dynamical systems by showing that the cyclic number of sign variations in the vector of derivatives is an integer-valued Lyapunov functio…
Optimal Translation Along a Circular mRNA
Yoram Zarai, Alexander Ovseevich, Michael Margaliot
The ribosome flow model on a ring (RFMR) is a deterministic model for translation of a circularized mRNA. We derive a new spectral representation for the optimal steady-state produ…
Ribosome Flow Model with Extended Objects
Yoram Zarai, Michael Margaliot, Tamir Tuller
We study a deterministic mechanistic model for the flow of ribosomes along the mRNA molecule, called the ribosome flow model with extended objects (RFMEO). This model encapsulates…
A Deterministic Model for One-Dimensional Excluded Flow with Local Interactions
Yoram Zarai, Michael Margaliot, Anatoly B. Kolomeisky
Natural phenomena frequently involve a very large number of interacting molecules moving in confined regions of space. Cellular transport by motor proteins is an example of such co…
A Deterministic Mathematical Model for Bidirectional Excluded Flow with Langmuir Kinetics
Yoram Zarai, Michael Margaliot, Tamir Tuller
In many important cellular processes, including mRNA translation, gene transcription, phosphotransfer, and intracellular transport, biological "particles" move along some kind of "…
On the Ribosomal Density that Maximizes Protein Translation Rate
Yoram Zarai, Michael Margaliot, Tamir Tuller
During mRNA translation, several ribosomes attach to the same mRNA molecule simultaneously translating it into a protein. This pipelining increases the protein production rate. A n…
Optimal Down Regulation of mRNA Translation
Yoram Zarai, Michael Margaliot, Tamir Tuller
Down regulation of mRNA translation is an important problem in various bio-medical domains ranging from developing effective medicines for tumors and for viral diseases to developi…
Controllability analysis and control synthesis for the ribosome flow model
Yoram Zarai, Michael Margaliot, Eduardo D. Sontag +1
The ribosomal density along the coding region of the mRNA molecule affect various fundamental intracellular phenomena including: protein production rates, organismal fitness, ribos…
Analyzing Linear Communication Networks using the Ribosome Flow Model
Yoram Zarai, Oz Mendel, Michael Margaliot
The Ribosome Flow Model (RFM) describes the unidirectional movement of interacting particles along a one-dimensional chain of sites. As a site becomes fuller, the effective entry r…
Ribosome Flow Model on a Ring
Alon Raveh, Yoram Zarai, Michael Margaliot +1
The asymmetric simple exclusion process (ASEP) is an important model from statistical physics describing particles that hop randomly from one site to the next along an ordered latt…
On the Structure of the Initiation and Elongation Rates that Maximize Protein Production in the Ribosome Flow Model
Yoram Zarai, Michael Margaliot
Translation is a crucial step in gene expression. During translation, macromolecules called ribosomes "read" the mRNA strand in a sequential manner and produce a corresponding prot…
Maximizing Protein Translation Rate in the Nonhomogeneous Ribosome Flow Model: A Convex Optimization Approach
Gilad Poker, Yoram Zarai, Michael Margaliot +1
Translation is an important stage in gene expression. During this stage, macro-molecules called ribosomes travel along the mRNA strand linking amino-acids together in a specific or…
Maximizing Protein Translation Rate in the Ribosome Flow Model: the Homogeneous Case
Yoram Zarai, Michael Margaliot, Tamir Tuller
Gene translation is the process in which intracellular macro-molecules, called ribosomes, decode genetic information in the mRNA chain into the corresponding proteins. Gene transla…
A Nonlinear Consensus Algorithm Derived from Statistical Physics
Michael Margaliot, Alon Raveh, Yoram Zarai
The asymmetric simple exclusion process (ASEP) is an important model from statistical physics describing particles that hop randomly from one site to the next along an ordered latt…