IEEE Transactions on NanoBioscience (IEEE T NANOBIOSCI )

Publisher: IEEE Engineering in Medicine and Biology Society, Institute of Electrical and Electronics Engineers

Description

This transaction reports on original, innovative and interdisciplinary work on all aspects of molecular systems, cellular systems, and tissues - including molecular electronics.

  • Impact factor
    1.29
    Show impact factor history
     
    Impact factor
  • 5-year impact
    1.75
  • Cited half-life
    5.90
  • Immediacy index
    0.21
  • Eigenfactor
    0.00
  • Article influence
    0.52
  • Website
    IEEE Transactions on NanoBioscience website
  • Other titles
    IEEE transactions on nanobioscience
  • ISSN
    1536-1241
  • OCLC
    47360509
  • Material type
    Periodical, Internet resource
  • Document type
    Journal / Magazine / Newspaper, Internet Resource

Publisher details

Institute of Electrical and Electronics Engineers

  • Pre-print
    • Author can archive a pre-print version
  • Post-print
    • Author can archive a post-print version
  • Conditions
    • Author's pre-print on Author's personal website, employers website or publicly accessible server
    • Author's post-print on Author's server or Institutional server
    • Author's pre-print must be removed upon publication of final version and replaced with either full citation to IEEE work with a Digital Object Identifier or link to article abstract in IEEE Xplore or replaced with Authors post-print
    • Author's pre-print must be accompanied with set-phrase, once submitted to IEEE for publication ("This work has been submitted to the IEEE for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessible")
    • Author's pre-print must be accompanied with set-phrase, when accepted by IEEE for publication ("(c) 20xx IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other users, including reprinting/ republishing this material for advertising or promotional purposes, creating new collective works for resale or redistribution to servers or lists, or reuse of any copyrighted components of this work in other works.")
    • IEEE must be informed as to the electronic address of the pre-print
    • If funding rules apply authors may post Author's post-print version in funder's designated repository
    • Author's Post-print - Publisher copyright and source must be acknowledged with citation (see above set statement)
    • Author's Post-print - Must link to publisher version with DOI
    • Publisher's version/PDF cannot be used
    • Publisher copyright and source must be acknowledged
  • Classification
    ​ green

Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: This paper investigates the exponential stability problem of switched stochastic genetic regulatory networks (GRNs) with time-varying delays. Two types of switched systems are studied respectively: one is the stochastic switched delayed GRNs with only stable subsystems and the other is the stochastic switched delayed GRNs with both stable and unstable subsystems. By using switching analysis techniques and the modified Halanay differential inequality, new criteria are developed for the exponential stability of switched stochastic GRNs with time-varying delays. Finally, an example is given to illustrate the main results.
    IEEE Transactions on NanoBioscience 09/2014; 13(3):336-342.
  • [Show abstract] [Hide abstract]
    ABSTRACT: To coordinate their behavior and virulence and to synchronize attacks against their hosts, bacteria communicate by continuously producing signaling molecules (called autoinducers) and continuously monitoring the concentration of these molecules. This communication is controlled by biological circuits called quorum sensing (QS) circuits. Recently QS circuits and have been recognized as an alternative target for controlling bacterial virulence and infections without the use of antibiotics. Pseudomonas aeruginosa is a Gram-negative bacterium that infects insects, plants, animals and humans and can cause acute infections. This bacterium has three interconnected QS circuits that form a very complex and versatile QS system, the operation of which is still under investigation. Here we use Boolean networks to model the complete QS system of Pseudomonas aeruginosa and we simulate and analyze its operation in both synchronous and asynchronous modes. The state space of the QS system is constructed and it turned out to be very large, hierarchical, modular and scale-free. Furthermore, we developed a simulation tool that can simulate gene knock-outs and study their effect on the regulons controlled by the three QS circuits. The model and tools we developed will give to life scientists a deeper insight to this complex QS system.
    IEEE Transactions on NanoBioscience 08/2014; 13(3):1-7.
  • [Show abstract] [Hide abstract]
    ABSTRACT: We report the extracellular biosynthesis of gold nanoparticles (AuNPs) using a fungus Fusarium acuminatum. Mycosynthesis of Au-NPs was carried out by challenging the fungal cells filtrate with HAuCl4 solution (1mM), as nanoparticles synthesizing enzyme secrete extracellularly by the fungi. The AuNPs were characterized with the help of UV-Visible spectrophotometer, Fourier Transform Infrared spectroscopy, Zeta Potential, X-ray diffraction (XRD) and Transmission electron microscopy (TEM). We observed absorbance peak in between 520 nm-550 nm corresponding to the surface plasmon absorbance of the gold nanoparticles. The nanoparticles synthesised in the present investigation were found to be capped by proteins. XRD results showed that the distinctive formation of crystalline gold nanoparticles in the solution. The spherical and polydispersed AuNPs in the range 8 to 28 nm with average size of 17 nm were observed by TEM analysis. We also standardised the parameters like the effect of pH, temperature and salt concentration on the biosynthesis of gold nanoparticles. It was found that acidic pH, 1mM salt concentration and 370C temperature were found to be optimum for the synthesis of Au-NPs. Therefore, the present study introduces the easy, better and cheaper method for biosynthesis of AuNPs.
    IEEE Transactions on NanoBioscience 08/2014;
  • [Show abstract] [Hide abstract]
    ABSTRACT: Nanoscale communication based on F¨orster Resonance Energy Transfer (FRET) enables nanoscale single molecular devices to communicate with each other utilizing excitons generated on fluorescent molecules as information carriers. Based on the point-to-point single-exciton FRET-based nanocommunication model, we investigate the multiple-exciton case for pointto- point and broadcast communications following an information theoretical approach and conducting simulations through Monte Carlo approach. We demonstrate that the multi-exciton transmission significantly improves the channel reliability and the range of the communication up to tens of nanometers for immobile nanonodes providing high data transmission rates. Furthermore, our analyses indicate that multi-exciton transmission enables broadcasting of information from a transmitter nanonode to many receiver nanonodes pointing out the potential of FRETbased communication to extend over nanonetworks. In this study, we also propose electrically and chemically controllable routing mechanisms exploiting the strong dependence of FRET rate on spectral and spatial characteristics of fluorescent molecules. We show that the proposed routing mechanisms enable the remote control of information flow in FRET-based nanonetworks. The high transmission rates obtained by multi-exciton scheme for point-to-point and broadcast communications, as well as the routing opportunities make FRET-based communication promising for future molecular computers.
    IEEE Transactions on NanoBioscience 07/2014;
  • [Show abstract] [Hide abstract]
    ABSTRACT: This paper describes a mobile bionanosensor network designed for target tracking. The mobile bionanosensor network is composed of bacterium-based autonomous biosensors that coordinate their movement through the use of two types of signaling molecules, repellents and attractants. In search of a target, the bacterium-based autonomous biosensors release repellents to quickly spread over the environment, while, upon detecting a target, they release attractants to recruit other biosensors in the environment toward the location around the target. A mobility model of bacterium-based autonomous biosensors is first developed based on the rotational diffusion model of bacterial chemotaxis, and from this their collective movement to track a moving target is demonstrated. In simulation experiments, the mobile bionanosensor network is evaluated based on the mean tracking time. Simulation results show a set of parameter values that can optimize the mean tracking time, providing an insight into how bacterium-based autonomous biosensors may be designed and engineered for target tracking.
    IEEE Transactions on NanoBioscience 07/2014;
  • [Show abstract] [Hide abstract]
    ABSTRACT: In this paper, we propose a symbol interval optimization algorithm in molecular communication with drift. Proper symbol intervals are important in practical communication systems since information needs to be sent as fast as possible with low error rates. There is a trade-off, however, between symbol intervals and inter-symbol interference (ISI) from Brownian motion. Thus, we find proper symbol interval values considering the ISI inside two kinds of blood vessels, and also suggest no ISI system for strong drift models. Finally, an isomer-based molecule shift keying (IMoSK) is applied to calculate achievable data transmission rates (achievable rates, hereafter). Normalized achievable rates are also obtained and compared in one-symbol ISI and no ISI systems.
    IEEE Transactions on NanoBioscience 07/2014;
  • [Show abstract] [Hide abstract]
    ABSTRACT: The reliable and accurate identification of cancer categories is crucial to a successful diagnosis and a proper treatment of the disease. In most existing work, samples of gene expression data are treated as one-dimensional signals, and are analyzed by means of some statistical signal processing techniques or intelligent computation algorithms. In this paper, from an image-processing viewpoint, a spectralfeature- based Tikhonov-regularized least-squares (TLS) ensemble algorithm is proposed for cancer classification using gene expression data. In the TLS model, a test sample is represented as a linear combination of the atoms of a dictionary. Two types of dictionaries, namely singular value decomposition (SVD)-based eigenassays and independent component analysis (ICA)-based eigenassays, are proposed for the TLS model, and both are extracted via a two-stage approach. The proposed algorithm is inspired by our finding that, among these eigenassays, the categories of some of the testing samples can be assigned correctly by using the TLS models formed from some of the spectral features, but not for those formed from the original samples only. In order to retain the positive characteristics of these spectral features in making correct category assignments, a strategy of classifier committee learning (CCL) is designed to combine the results obtained from the different spectral features. Experimental results on standard databases demonstrate the feasibility and effectiveness of the proposed method.
    IEEE Transactions on NanoBioscience 06/2014;
  • [Show abstract] [Hide abstract]
    ABSTRACT: Nanonetworks refer to a group of nano-sized machines with very basic operational capabilities communicating to each other in order to accomplish more complex tasks such as in-body drug delivery, or chemical defense. Realizing reliable and high-rate communication between these nanomachines is a fundamental problem for the practicality of these nanonetworks. Recently, we have proposed a molecular communication method based on F¨orster Resonance Energy Transfer (FRET) which is a nonradiative excited state energy transfer phenomenon observed among fluorescent molecules, i.e., fluorophores. We have modeled the FRET-based communication channel considering the fluorophores as single-molecular immobile nanomachines, and shown its reliability at high rates, and practicality at the current stage of nanotechnology. In this study, for the first time in the literature, we investigate the network of mobile nanomachines communicating through FRET. We introduce two novel mobile molecular nanonetworks: FRET-based mobile molecular sensor/actor nanonetwork (FRET-MSAN) which is a distributed system of mobile fluorophores acting as sensor or actor node; and FRET-based mobile ad hoc molecular nanonetwork (FRETMAMNET) which consists of fluorophore-based nanotransmitter, nanoreceivers and nanorelays. We model the single message propagation based on birth-death processes with continuous time Markov chains. We evaluate the performance of FRETMSAN and FRET-MAMNET in terms of successful transmission probability and mean extinction time of the messages, system throughput, channel capacity and achievable communication rates.
    IEEE Transactions on NanoBioscience 06/2014;
  • IEEE Transactions on NanoBioscience 06/2014; 13(2):63-4.
  • [Show abstract] [Hide abstract]
    ABSTRACT: To coordinate their behavior and virulence and to synchronize attacks against their hosts, bacteria communicate by continuously producing signaling molecules (called autoinducers) and continuously monitoring the concentration of these molecules. This communication is controlled by biological circuits called quorum sensing (QS) circuits. Recently QS circuits and have been recognized as an alternative target for controlling bacterial virulence and infections without the use of antibiotics. Pseudomonas aeruginosa is a Gram-negative bacterium that infects insects, plants, animals and humans and can cause acute infections. This bacterium has three interconnected QS circuits that form a very complex and versatile QS system, the operation of which is still under investigation. Here we use Boolean networks to model the complete QS system of Pseudomonas aeruginosa and we simulate and analyze its operation in both synchronous and asynchronous modes. The state space of the QS system is constructed and it turned out to be very large, hierarchical, modular and scale-free. Furthermore, we developed a simulation tool that can simulate gene knock-outs and study their effect on the regulons controlled by the three QS circuits. The model and tools we developed will give to life scientists a deeper insight to this complex QS system.
    IEEE Transactions on NanoBioscience 01/2014; 13(3):343-349.
  • [Show abstract] [Hide abstract]
    ABSTRACT: During the last decade, the advent of Ontologies used for biomedical annotation has had a deep impact on life science. MeSH is a well-known Ontology for the purpose of indexing journal articles in PubMed, improving literature searching on multi-domain topics. Since the explosion of data growth in recent years, there are new terms, concepts that weed through the old and bring forth the new. Automatically extending sets of existing terms will enable bio-curators to systematically improve text-based ontologies level by level. However, most of the related techniques which apply symbolic patterns based on a literature corpus tend to focus on more general but not specific parts of the ontology. Therefore, in this work, we present a novel method for utilizing genealogical information from Ontology itself to find suitable siblings for ontology extension. Based on the breadth and depth dimensions, the sibling generation stage and pruning strategy are proposed in our approach. As a result, on the average, the precision of the genealogical-based method achieved 0.5, with the best 0.83 performance of category “Organisms.” We also achieve average precision 0.69 of 229 new terms in MeSH 2013 version.
    IEEE Transactions on NanoBioscience 01/2014; 13(2):124-130.
  • [Show abstract] [Hide abstract]
    ABSTRACT: DNA microarray data now permit scientists to screen thousand of genes simultaneously and determine whether those genes are active or silent in normal and cancerous tissues. With the advancement of microarray technology, new analytical methods must be developed to find out whether microarray data have discriminative signatures of gene expression over normal or cancerous tissues. In this paper, we attempt a prediction scheme that combines fuzzy preference based rough set (FPRS) method for feature (gene) selection with semisupervised SVMs. To show the effectiveness of the proposed approach, we compare the performance of this technique with the signal-to-noise ratio (SNR) and consistency based feature selection (CBFS) methods. Using six benchmark gene microarray datasets (including both binary and multi-class classification problems), we demonstrate experimentally that our proposed scheme can achieve significant empirical success and is biologically relevant for cancer diagnosis and drug discovery.
    IEEE Transactions on NanoBioscience 01/2014; 13(2):152-160.
  • [Show abstract] [Hide abstract]
    ABSTRACT: Recently, statistics and machine learning have been developed to identify functional or taxonomic features of environmental features or physiological status. Important proteins (or other functional and taxonomic entities) to environmental features can be potentially used as biosensors. A major challenge is how the distribution of protein and gene functions embodies the adaption of microbial communities across environments and host habitats. In this paper, we propose a novel regularization method for linear regression to adapt the challenge. The approach is inspired by local linear embedding (LLE) and we call it a manifold-constrained regularization for linear regression (McRe). The novel regularization procedure also has potential to be used in solving other linear systems. We demonstrate the efficiency and the performance of the approach in both simulation and real data.
    IEEE Transactions on NanoBioscience 01/2014; 13(2):104-108.
  • [Show abstract] [Hide abstract]
    ABSTRACT: Although the subject of some scrutiny over the years, the mechanism of conduction in DNA has not yet been resolved, with competing theories suggesting either electronic and ionic conduction mechanisms. In this paper we use dielectrophoresis to determine the electrical properties of poly(dG)-poly(dC) (GC) and poly(dA)-poly(dT) (AT) DNA in solution. The molecules show different conduction mechanisms; GC DNA exhibits conduction primarily through the molecule, whereas in AT DNA conduction through the counterion cloud surrounding the molecule in solution is more significant.
    IEEE Transactions on NanoBioscience 01/2014; 13(1):51-54.