13 papers · ranked by Valyu relevance
Prasad U. Bandodkar, Razeen R. Shaikh, Gregory T. Reeves
Model development is essential to gain a mathematical understanding of the underlying phenomena in systems biology. In most models, it is typically hard to estimate the values of the biophysical/phenomenological parameters that characterize the model. The parameters are estimated by minimizing a function that reduces a…
Pai Li, Ze Zhang, Brad Day, Yiying Tong
The eukaryotic cytoskeleton plays essential roles in cell signaling, trafficking, and motion. Recent work towards defining the temporal and spatial dynamics of cytoskeletal organization, including as a function of cell status, has utilized quantitative analysis of cytoskeletal fluorescence images as a standard approach…
Fotios Drakopoulos, Viacheslav Vasilkov, Alejandro Osses Vecchi, Tijmen Wartenberg + 1 more
It is well known that ageing and noise exposure are important causes of sensorineural hearing loss, and can result in damage of the outer hair cells or other structures of the inner ear, including synaptic damage to the auditory nerve (AN), i.e., cochlear synaptopathy (CS). Despite the suspected high prevalence of CS…
Minindu Weerakoon, Christopher T Saunders, Haynes Heaton
Most multiple sequence alignment and string-graph alignment algorithms focus on global alignment, but many applications exist for semi-global and local string-graph alignment. Long reads require enormous amounts of memory and runtime to fill out large dynamic programming tables. Effective algorithms for finding the…
Subarna Sasmal, Martin McCullagh, Glen M. Hocky
Our ability to efficiently sample conformational transitions between two known states of a biomolecule using collective variable (CV) based sampling depends strongly on the choice of the CV. We previously reported a data-driven approach to clustering biomolecular configurations with a probabilistic clustering model…
Azadeh Hassanpour, Antje Rohde, Henner Simianer, Torsten Pook
Plant breeding is a complex process that involves trade-offs among competing breeding objectives and limited resources. Despite the necessity for optimization of breeding program design, the inherent complexity can make optimization challenging. Most often, a predefined set of scenarios is compared or a single…
Mathias Gotsmy, Dafni Giannari, Radhakrishnan Mahadevan, Jürgen Zanghellini
Fed-batch processes are prevalent in biotechnological industries, but design of experiments often results in sub-optimal conditions due to incomplete solution space characterization. We employ a single-level dynamic control (DC) algorithm for dynamic flux balance analysis (dFBA), enhancing efficiency by reducing…
Timothy L. Bailey, Charles E. Grant
Motif enrichment algorithms can identify known sequence motifs that are present to a statistically significant degree in DNA, RNA and protein sequences. Databases of such known motifs exist for DNA- and RNA-binding proteins, as well as for many functional protein motifs. The SEA (“Simple Enrichment Analysis”) algorithm…
Lillian T. Tatka, Lucian P. Smith, Herbert M. Sauro
Evolutionary algorithms, a class of optimization techniques inspired by biological evolution, have emerged as powerful tools for the optimization of complex systems, including the evolution of mass-action chemical reaction networks. This work explores the application of evolutionary algorithms in this domain…
Ibrahim Ihsan Taskiran, Katina I. Spanier, Valerie Christiaens, David Mauduit + 1 more
Transcriptional enhancers act as docking stations for combinations of transcription factors and thereby regulate spatiotemporal activation of their target genes. A single enhancer, of a few hundred base pairs in length, can autonomously and independently of its location and orientation drive cell-type specific…
Curtis Goolsby, Ashkan Fakharzadeh, Mahmoud Moradi
We have formulated a Riemannian framework for describing the geometry of collective variable spaces of biomolecules within the context of collective variable based molecular dynamics simulations. The formalism provides a theoretical framework to develop enhanced sampling techniques, path-finding algorithms, and…
Changin Oh, Kathleen P. Wilkie
We present the Toroidal Search Algorithm (TSA), a novel population-based metaheuristic optimization method inspired by the topology of a torus. Conventional metaheuristics frequently suffer from boundary stagnation, a phenomenon that severely degrades performance in bounded and high-dimensional search spaces. TSA…
Martín Gutiérrez, Yerko Ortiz, Javier Carrión
Metaheuristic procedures (MH) have been a trend driving Artificial Intelligence (AI) researchers for the past 50 years. A variety of tools and applications (not only in Computer Science) stem from these techniques. Also, MH frequently rely on evolution, a trademark process involved in cell colony growth. Generally, MH…