Related papers: On the remote interaction of biological objects wi…
We use simple analytic arguments and lattice-based computer simulations to study the growth of structures made from a large number of distinct component types. Components possess 'designed' interactions, chosen to stabilize an equilibrium…
We have used the Monte Carlo based computer models to show that selection pressure could affect the distribution of recombination hotspots along the chromosome. Close to critical crossover rate, where genomes may switch between the…
Our work is motivated by and illustrated with application of association networks in computational biology, specifically in the context of gene/protein regulatory networks. Association networks represent systems of interacting elements,…
We present a general theory for predicting the interaction potentials between DNA-coated colloids, and more broadly, any particles that interact via valence-limited ligand-receptor binding. Our theory correctly incorporates the…
The increasing interest in understanding the behavior of the biological neural networks, and the increasing utilization of artificial neural networks in different fields and scales, both require a thorough understanding of how neuromorphic…
The continuity of life and its evolution, we proposed, emerge from an interactive group process manifested in networks of interaction. We term this process \textit{survival-of-the-fitted}. Here, we reason that survival of the fitted results…
Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…
Despite the earlier claim of "Death of Distance", recent studies revealed that geographical proximity still greatly influences link formation in online social networks. However, it is unclear how physical distances are intertwined with…
This paper describes an approach that combines generative adversarial networks (GANs) with interactive evolutionary computation (IEC). While GANs can be trained to produce lifelike images, they are normally sampled randomly from the learned…
Today, people use multiple devices to fulfill their information needs. However, designers design each device individually, without accounting for the other devices that users may also use. In many cases, the applications on all these…
In this paper we investigate the evolution of cooperation when the interaction structure is strictly local, and hence fitness only depends on local behaviors, while the competition structure is partly global, and hence selection can happen…
In the real world, most objects and data have multiple types of attributes and inter-connections. Such data structures are named "Heterogeneous Information Networks" (HIN) and have been widely researched. Biological systems are also…
Exchange interaction strongly influences the long-range behavior of localized electron orbitals and quantum tunneling amplitudes.In the Hartree-Fock approximation the exchange produces a power-law decay instead of the usual exponential…
The living-together of distinct organisms in a single termite nest along with the termite builder colony, is emblematic in its ecological and evolutionary significance. On top of preserving biodiversity, these interspecific and…
Machine learning can have major societal impact in computational biology applications. In particular, it plays a central role in the development of precision medicine, whereby treatment is tailored to the clinical or genetic features of the…
The ability to measure or manipulate network connectivity is the main challenge in the field of connectomics. Recently, a set of approaches has been developed that takes advantage of next generation DNA sequencing to scan connections…
This work proposes a unified framework to leverage biological information in network propagation-based gene prioritization algorithms. Preliminary results on breast cancer data show significant improvements over state-of-the-art baselines,…
Although species longevity is subject to a diverse range of selective forces, the mortality curves of a wide variety of organisms are rather similar. We argue that aging and its universal characteristics may have evolved by means of a…
We live within an increasingly technological, information-laden environment for the first time in human evolution.This subjects us, and will continue to subject us in an accelerating fashion, to an unremitting exposure to meaningful…
We introduce network $L$-cloning, a technique for creating ensembles of random networks from any given real-world or artificial network. Each member of the ensemble is an $L$-cloned network constructed from $L$ copies of the original…