分子网络
Recent studies suggest that PML (Promyelocytic Leukemia) suppresses p53 protein degradation by inhibiting MDM2 protein in the nucleus [1], and regulates a number of biological functions [2]. We modeled a PML-MDM2-p53 regulatory network by…
Complex biological systems have been successfully modeled by biochemical and genetic interaction networks, typically gathered from high-throughput (HTP) data. These networks can be used to infer functional relationships between genes or…
A key aim of systems biology is the reconstruction of molecular networks, however we do not yet have networks that integrate information from all datasets available for a particular clinical condition. This is in part due to the limited…
Across many fields, a problem of interest is to predict the transition rates between nodes of a network, given limited stationary state and dynamical information. We give a solution using the principle of Maximum Caliber. We find the…
Pseudomonas aeruginosa is a metabolically flexible member of the Gammaproteobacteria. Under anaerobic conditions and the presence of nitrate, P. aeruginosa can perform (complete) denitrification, a respiratory process of dissimilatory…
Chemistry as an unconventional computing medium presently lacks a systematic approach to gather, store, and sort data over time. To build more complicated systems in chemistries, the ability to look at data in the past would be a valuable…
The tumor suppressor p53 plays a central role in cell fate decisions after DNA damage. Programmed Cell Death 5 (PDCD5) is known to interact with the p53 pathway to promote cell apoptosis. Recombinant human PDCD5 can significantly sensitize…
Dynamics of p53 is known to play important roles in the regulation of cell fate decisions in response to various stresses, and PDCD5 functions as a co-activator of p53 to modulate the p53 dynamics. In the present paper, we investigate how…
The importance of studying properties of networks is manifest in diverse fields ranging from biology, engineering, physics, chemistry, neuroscience, and medicine. The functionality of networks with regard to performance, throughput,…
Bow-tie or hourglass structure is a common architectural feature found in biological and technological networks. A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output…
The quantum network model with real variables is usually used to describe the excitation energy transfer (EET) in the Fenna-Matthews-Olson(FMO) complexes. In this paper we add the quantum phase factors to the hopping terms and find that the…
Dynamics in biological networks are in general robust against several perturbations. We investigate a coupled map network as a model motivated by gene regulatory networks and design systems which are robust against phenotypic perturbations…
The family of TGFb ligands is large and its members are involved in many different signaling processes. These signaling processes strongly differ in type with TGFb ligands eliciting both sustained or transient responses. Members of the TGFb…
Motivation: Identifying the molecular pathways more prone to disruption during a pathological process is a key task in network medicine and, more in general, in systems biology. Results: In this work we propose a pipeline that couples a…
We establish that mass conserving single terminal-linkage networks of chemical reactions admit positive steady states regardless of network deficiency and the choice of reaction rate constants. This result holds for closed systems without…
Gene regulatory networks arise in all living cells, allowing the control of gene expression patterns. The study of their topology has revealed that certain subgraphs of interactions or "motifs" appear at anomalously high frequencies. We ask…
Bistability plays a central role in the gene regulatory networks (GRNs) controlling many essential biological functions, including cellular differentiation and cell cycle control. However, establishing the network topologies that can…
Recent whole genome polymerase binding assays have shown that a large proportion of unexpressed genes have pre-assembled RNA pol II transcription initiation complex stably bound to their promoters. Some such promoter proximally paused genes…
\textit{Vibrio harveyi} and \textit{Vibrio cholerae} have quorum sensing pathways with similar design and highly homologous components including multiple small RNAs (sRNAs). However, the associated luminescence phenotypes of strains with…
Stochastic modelling provides an indispensable tool for understanding how random events at the molecular level influence cellular functions. In practice, the common challenge is to calibrate a large number of model parameters against the…