6 citations · 10 across the 4 of their papers we have counts for
7 papers
Newton-Okounkov bodies of chemical reaction systems
Nida Obatake, Elise Walker
Despite their noted potential in polynomial-system solving, there are few concrete examples of Newton-Okounkov bodies arising from applications. Accordingly, in this paper, we intr…
Mixed volume of small reaction networks
Nida Obatake, Anne Shiu, Dilruba Sofia
An important invariant of a chemical reaction network is its maximum number of positive steady states. This number, however, is in general difficult to compute. Nonetheless, there…
Dynamics of ERK regulation in the processive limit
Carsten Conradi, Nida Obatake, Anne Shiu +1
We consider a model of extracellular signal-regulated kinase (ERK) regulation by dual-site phosphorylation and dephosphorylation, which exhibits bistability and oscillations, but l…
Identifiability of Linear Compartmental Models: The Effect of Moving Inputs, Outputs, and Leaks
Seth Gerberding, Nida Obatake, Anne Shiu
A mathematical model is identifiable if its parameters can be recovered from data. Here we investigate, for linear compartmental models, whether (local, generic) identifiability is…
Oscillations and bistability in a model of ERK regulation
Nida Obatake, Anne Shiu, Xiaoxian Tang +1
This work concerns the question of how two important dynamical properties, oscillations and bistability, emerge in an important biological signaling network. Specifically, we consi…
On the identification of -inductively pierced codes using toric ideals
Molly Hoch, Samuel Muthiah, Nida Obatake
Neural codes are binary codes in ; here we focus on the ones which represent the firing patterns of a type of neurons called place cells. There is much interest in deter…