Related papers: Automatically layout and visualize the biological …
Path graphs are intersection graphs of paths in a tree. We start from the characterization of path graphs by Monma and Wei [C.L.~Monma,~and~V.K.~Wei, Intersection Graphs of Paths in a Tree, J. Combin. Theory Ser. B, 41:2 (1986) 141--181]…
Cities can be seen as the epitome of complex systems. They arise from a set of interactions and components so diverse that is almost impossible to describe them exhaustively. Amid this diversity, we chose an object which orchestrates the…
The pathway idea is a way of going from one family of functions to another family of functions and yet another family of functions through a parameter in the model so that a switching mechanism is introduced into the model through a…
Cellular response to a perturbation is the result of a dynamic system of biological variables linked in a complex network. A major challenge in drug and disease studies is identifying the key factors of a biological network that are…
Large graphs can be found in a wide array of scientific fields ranging from sociology and biology to scientometrics and computer science. Their analysis is by no means a trivial task due to their sheer size and complex structure. Such…
A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…
Biomolecular networks have already found great utility in characterizing complex biological systems arising from pair-wise interactions amongst biomolecules. Here, we review how graph theoretical approaches can be applied not only for a…
Networks provide a meaningful way to represent and analyze complex biological information, but the methodological details of network-based tools are often described for a technical audience. Graphery is a hands-on tutorial webserver…
Signalling pathways are abstractions that help life scientists structure the coordination of cellular activity. Cross-talk between pathways accounts for many of the complex behaviours exhibited by signalling pathways and is often critical…
A prototype for a web application was designed and implemented as a guide to be used by clinicians when designing the best drug therapy for a specific cancer patient, given biological data derived from the patients tumor tissue biopsy. A…
A system level view of cellular processes for human and several organisms can be cap- tured by analyzing molecular interaction networks. A molecular interaction network formed of differentially expressed genes and their interactions helps…
We view molecular optimization as a graph-to-graph translation problem. The goal is to learn to map from one molecular graph to another with better properties based on an available corpus of paired molecules. Since molecules can be…
In this paper, we present a survey of the use of graph theoretical techniques in Biology. In particular, we discuss recent work on identifying and modelling the structure of bio-molecular networks, as well as the application of centrality…
Graph drawing addresses the problem of finding a layout of a graph that satisfies given aesthetic and understandability objectives. The most important objective in graph drawing is minimization of the number of crossings in the drawing, as…
Affordable, high-quality whole-genome assemblies have made it possible to construct rich pangenomes that capture haplotype diversity across many species. As these datasets grow, they motivate the development of specialized techniques…
Modern high-throughput gene perturbation screens are key technologies at the forefront of genetic research. Combined with rich phenotypic descriptors they enable researchers to observe detailed cellular reactions to experimental…
Modern methods of graph theory describe a graph up to isomorphism, which makes it difficult to create mathematical models for visualizing graph drawings on a plane. The topological drawing of the planar part of a graph allows representing…
This book collects the lectures about graph theory and its applications which were given to students of mathematical departments of Moscow State University and Peking University. Graph theory is a very wide field with a lot of applications…
Pathway idea is a switching mechanism by which one can go from one functional form to another, and to yet another. It is shown that through a parameter $\alpha$, called the pathway parameter, one can connect generalized type-1 beta family…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…