A Fast Sequence Assembly Method Based on Compressed Data Structures

Liang, Peifeng ;   Zhang, Yancong ;   Lin, Kui ;   Hu, Jinglu

Tags Algorithms and techniques for systems modeling

Assembling a large genome using next generation sequencing reads requires large computer memory and a long execution time. To reduce these...

Read More Download this Paper

A Full-Wave Phase Aberration Correction Method for Transcranial High-Intensity Focused Ultrasound Brain Therapies

Almquist, Scott ;   de Bever, Joshua ;   Merrill, Robb ;   Parker, Dennis ;   Christensen, Douglas

Tags Algorithms and techniques for systems modelingMedical device modeling

Transcranial high-intensity focused ultrasound has recently been used to noninvasively treat several types of brain disorders. However, due...

Read More Download this Paper

A Method for Modeling Oxygen Diffusion in an Agent-Based Model

Sershen, Cheryl ;   Plimpton, Steven ;   May, Elebeoba

Tags Algorithms and techniques for systems modelingMultiscale modelingModeling of biomolecular system dynamics

This paper describes a method for incorporating a chemotactic diffusion field into an agent-based model (ABM). Our method for modeling...

Read More Download this Paper

A Novel Extreme Learning Machine for Hypoglycemia Detection

San, Phyo Phyo ;   Ling, Steve ;   Soe, Ni Ni ;   Nguyen, Hung T.

Tags Algorithms and techniques for systems modelingMedical decision making

Hypoglycemia is a common side-effect of insulin therapy for patients with type 1 diabetes mellitus (T1DM) and is the major limiting factor to...

Read More Download this Paper

Analysis of the HIV Eradication Phenomenon at the Early Stage of Infection with an Extracellular Deterministic Model

Chang, H.J. ;   Moog, Claude ;   Astolfi, Alessandro

Tags Algorithms and techniques for systems modelingPK/PDClinical applications of biological networks

We investigate the phenomenon of HIV eradication at the early stage of the infection and evaluate the chance of the eradication with a...

Read More Download this Paper

Biologically-Motivated System Identification: Application to Microbial Growth Modeling

Yan, Jinyao ;   Deller, John

Tags Algorithms and techniques for systems modelingParameter estimationNetwork modeling

This paper presents a new method for identification of system models that are linear in parametric structure, but arbitrarily nonlinear in...

Read More Download this Paper

Latent Force Models for Describing Transcriptional Regulation Processes in the Embryo Development Problem for the Drosophila Melanogaster

Vasquez Jaramillo, Juan David ;   Alvarez, Mauricio A. ;   Orozco, Alvaro

Tags Algorithms and techniques for systems modelingModeling of gene/epigene regulatory networks

In the embryo development problem for the Drosophila melanogaster, a set of molecules known as morphogens are responsible for the embryo...

Read More Download this Paper

Modeling Collective & Intelligent Decision Making of Multi-Cellular Populations

Shin, Yong-Jun ;   Mahrou, Bahareh

Tags Algorithms and techniques for systems modelingNetwork modelingAdvances in theory of biological networks

In the presence of unpredictable disturbances and uncertainties, cells intelligently achieve their goals by sharing information via cell-cell...

Read More Download this Paper

Polynomial Chaos Decomposition Applied to Stochastic Dosimetry: Study of the Influence of the Magnetic Field Orientation on the Pregnant Woman Exposure at 50 Hz

Liorni, Ilaria ;   Parazzini, Marta ;   Fiocchi, Serena ;   Guadagnin, Vanessa ;   Ravazzani, Paolo

Tags Algorithms and techniques for systems modelingParameter estimationPhysiological systems

Polynomial Chaos (PC) is a decomposition method used to build a meta-model, which approximates the unknown response of a model. In this paper...

Read More Download this Paper

Specifying Informative Experiment Stimulation Conditions for Resolving Dynamical Uncertainty in Biological Systems

Mdluli, Thembi ;   Pargett, Michael ;   Buzzard, Greg T. ;   Rundell, Ann E.

Tags Algorithms and techniques for systems modelingParameter estimationBiomedical data-driven modeling

A computationally efficient model-based design of experiments (MBDOE) strategy is developed to plan an optimal experiment by specifying the...

Read More Download this Paper

Supervised Method for Construction of Microrna-Mrna Networks: Application in Cardiac Tissue Aging Dataset

Dimitrakopoulos, Georgios ;   Dimitrakopoulou, Konstantina ;   Maraziotis, Ioannis ;   Sgarbas, Kyriakos ;   Bezerianos, Anastasios

Tags Algorithms and techniques for systems modelingNetwork modelingAnalysis of high-throughput systems biology data

MicroRNAs play an important role in regulation of gene expression, but still detection of their targets remains a challenge. In this work we...

Read More Download this Paper

Using Metabolomic and Transportomic Modeling and Machine Learning to Identify Putative Novel Therapeutic Targets for Antibiotic Resistant Pseudomonad Infections

Larsen, Peter ;   Collart, Frank ;   Dai, Yang

Tags Clinical applications of biological networksModeling of biomolecular system pathwaysAlgorithms and techniques for systems modeling

Hospital acquired infections sicken or kill tens of thousands of patients every year. These infections are difficult to treat due to a growing...

Read More Download this Paper