Molecular Networks
Neoplasms (NPs) and neurological diseases and disorders (NDDs) are amongst the major classes of diseases underlying deaths of a disproportionate number of people worldwide. To determine if there exist some distinctive features in the local…
Gene expression datasets consist of thousand of genes with relatively small samplesizes (i.e. are large-$p$-small-$n$). Moreover, dependencies of various orders co-exist in the datasets. In the Undirected probabilistic Graphical Model (UGM)…
In a highly simplified view, a disease can be seen as the phenotype emerging from the interplay of genetic predisposition and fluctuating environmental stimuli. We formalize this situation in a minimal model, where a network (representing…
Protein subcellular localization is an important factor in normal cellular processes and disease. While many protein localization resources treat it as static, protein localization is dynamic and heavily influenced by biological context.…
Our Microbiome Network Alignment Algorithm (MiNAA) aligns two microbial networks using a combination of the GRAph ALigner (GRAAL) algorithm and the Hungarian algorithm. Network alignment algorithms find pairs of nodes (one node from the…
Long-term behaviors of biochemical systems are described by steady states in deterministic models and stationary distributions in stochastic models. Obtaining their analytic solutions can be done for limited cases, such as linear or…
Long non-coding RNAs (lncRNAs) are important regulators to modulate gene expression and cell proliferation in the developing human brain. Previous methods mainly use bulk lncRNA and mRNA expression data to study lncRNA regulation. However,…
Network Medicine has improved the mechanistic understanding of disease, offering quantitative insights into disease mechanisms, comorbidities, and novel diagnostic tools and therapeutic treatments. Yet, most network-based approaches rely on…
DNA computing, a nontraditional computing mechanism, provides a feasible and effective method for solving NP-hard problems because of the vast parallelism and high-density storage of DNA molecules. Although DNA computing has been exploited…
In this paper, we tested several sparse optimization algorithms based on the public dataset of the DREAM5 Gene Regulatory Network Inference Challenge. And we find that introducing 20% of the regulatory network as a priori known data can…
Cell signaling networks are complex and often incompletely characterized, making it difficult to obtain a comprehensive picture of the mechanisms they encode. Mathematical modeling of these networks provides important clues, but the models…
The sequential probability ratio test (SPRT) from statistics is known to have the least mean decision time compared to other sequential or fixed-time tests for given error rates. In some circumstances, cells need to make decisions…
Morphogenesis, the establishment and repair of emergent complex anatomy by groups of cells, is a fascinating and biomedically-relevant problem. One of its most fascinating aspects is that a developing embryo can reliably recover from…
Inference of gene regulatory networks has been an active area of research for around 20 years, leading to the development of sophisticated inference algorithms based on a variety of assumptions and approaches. With the always increasing…
The emergence of and transitions between distinct phenotypes in isogenic cells can be attributed to the intricate interplay of epigenetic marks, external signals, and gene regulatory elements. These elements include chromatin remodelers,…
With the advent of high-throughput sequencing (HTS) in molecular biology and medicine, the need for scalable statistical solutions for modeling complex biological systems has become of critical importance. The increasing number of platforms…
There are two phases of Wnt signalling in early vertebrate embryogenesis: very early, maternal Wnt signalling promotes dorsal development, and slightly later, zygotic Wnt signalling promotes ventral and lateral mesoderm induction. However,…
Cells sense their surrounding by employing intracellular signaling pathways that transmit hormonal signals from the cell membrane to the nucleus. TGF-$\beta$/SMAD signaling encodes various cell fates, controls tissue homeostasis and is…
Metabolic fluxes in cells are governed by physical, physiological, and economic principles. Here I assume an optimal allocation of enzyme resources and postulate a general principle for metabolism: each enzyme must convert less valuable…
Circadian rhythms are biological rhythms of approximately 24 h that persist even under constant conditions without environmental daily cues. The molecular circadian clock machinery generates the physiological rhythms, which can be…