Transactions on NanoBioscience
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Principles of Information Storage in Small-Molecule Mixtures
Molecular data systems have the potential to store information at dramatically higher density than existing electronic media. Some of the first experimental demonstrations of this idea have used DNA, but nature also uses a wide diversity of smaller non-polymeric molecules... Read more
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Stability and oscillation analysis of a gene regulatory network with multiple time delays and diffusion rate
In genetic regulatory networks (GRNs), the diffusion rate of mRNA and protein play a key role in regulatory mechanisms of gene expression, especially in translation and transcription. However, the influence of diffusion rate on oscillatory gene expression is not well... Read more
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Uncovering the dynamic mechanisms of the Pseudomonas aeruginosa quorum sensing and virulence networks using Boolean modelling
Pseudomonas aeruginosa is an opportunistic pathogen with a large repertoire of virulence factors that allow it to cause acute and chronic infections. Treatment of P. aeruginosa infections often fail due to its antibiotic resistance mechanisms, thus novel strategies aim at... Read more
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Local Synchronization on Asynchronous Tissue P Systems with Symport/Antiport Rules
Asynchronous tissue P systems with symport/antiport rules are a class of parallel computing models inspired by cell tissue working in a non-synchronized way, where the use of rules is not obligatory, that is, at a computation step, an enabled rule... Read more
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New Method to Global Exponential Stability Analysis for Switched Genetic Regulatory Networks with Mixed Delays
In this paper, the sufficient conditions for the global exponential stability of the switched genetic regulatory networks with mixed time delays are obtained. The proposed method does not need the construction of Lyapunov–Krasovskii functional, but is directly proceeded by the... Read more
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Low-Complexity Adaptive Signal Detection for Mobile Molecular Communication
Currently, most of the researches in molecular communication (MC) domain focus on the static MC scenarios. However, some envisioned important MC applications require mobile MC system. The investigation on mobile MC, especially the signal detection of mobile MC is limited.... Read more
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Adjusting Linking Strands to Form Size-Controllable DNA Origami Rings
DNA origami is a powerful tool in nanotechnology that can be used to construct arbitrary structures for several nanoengineering applications. Generally, the more complex and sophisticated the construction, the greater is the number of origamis and connection strands that will... Read more
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Utilizing Neurons for Digital Logic Circuits: A Molecular Communications Analysis
With the advancement of synthetic biology, several new tools have been conceptualized over the years as alternative treatments for current medical procedures. This work we investigate how synthetically engineered neurons can operate as digital logic gates that can be used... Read more
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Constraining DNA sequences with a triplet-bases unpaired
DNA computing, the combination of computer science and molecular biology, is a burgeoning research field that holds promise for many applications. The accuracy of DNA computing is determined by reliable DNA sequences, the quality of which affects the accuracy of... Read more
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Sol-Gel Based Electrospray Synthesis of Barium Titanate Nanoparticles
Barium titanate nanoparticles are desirable for a wide range of applications, spanning electronics to biomedicine. Here, we present and electrospray-based method for the synthesis of barium titanate nanomaterials, where their morphology can be altered, forming either particles or rods. Aselectrosprayed... Read more
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Information-Theoretic Model and Analysis of Molecular Signaling in Targeted Drug Delivery
Targeted drug delivery (TDD) modality promises a smart localization of appropriate dose of therapeutic drugs to the targeted part of the body at reduced system toxicity. To achieve the desired goals of TDD, accurate analysis of the system is important.... Read more
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Synthesis of La-Sr-Mn-O and La-Sr-Ca-Mn-O perovskites through solution combustion using urea at fuel deficient conditions
La0.7Sr0.3MnO3 (LSMO) nanoparticles have been obtained via solution combustion synthesis (SCS) using urea and glycine as fuels. Also, La0.7Sr0.27Ca0.03MnO3 (LSCMO) nanoparticles have been synthesized through solution combustion using urea as fuel. In this paper, the combustion process was carried out... Read more
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Special Section on Advances in NanoBioEngineering ICNBE 2018
In 2018, the IEEE EMBS R9 Monterrey Chapter co-sponsored the first edition of the International Congress on NanoBioEngineering (ICNBE´18), organized by the Universidad Autonoma de Nuevo Leon through the School of Chemical Sciences, as the inaugural event of their new... Read more
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Special Section on IEEE EMBS Conference on Micro and Nanotechnology in Medicine
The 4th IEEE EMBS Conference on Micro and Nanotechnology in Medicine was held in Kauai, Hawaii, on December 10–14, 2018. This meeting gathered together 200 scientists, engineers, entrepreneurs, and medical researchers to leverage our collective expertise towards developing improved biomedical... Read more
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Special Section on Molecular Communications for Interfacing and Modeling Living Systems
Molecular communications (MolCom) has been established as one of the novel interdisciplinary research themes with strong impact on science and technology in the last five years. For this reason, in 2016 the European Project CIRCLE (Coordinating European Research on Molecular... Read more
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Editorial: All grown up with volume 18 in 2019!
The IEEE Transactions on NanoBioscience thank its reviewers, editorial board members, and most importantly its authors and readers for their support in 2018 and wishes them all the best for 2019! The Transactions finished 2018 with 200 submitted manuscripts, 62 articles... Read more
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Molecular Communication: A Personal Perspective
The authors of this paper have been involved in molecular communication since its conception. They describe their decade-and-a-half long personal journey of the molecular communication research and share their observations and thoughts on how the molecular communication research started and... Read more
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Paper-Based Membraneless Co-Laminar Microfluidic Glucose Biofuel Cell With MWCNT-Fed Bucky Paper Bioelectrodes
The present work establishes a membraneless, co-laminar flow-based approach to develop a cost-effective microfluidic paper-based analytical device for enzymatic biofuel cell (µPAD-EBFC). The developed µPAD-EBFC supporting the self-capillary fluid transport action, consists of Y-shaped paper microchannel with the fuel (glucose)... Read more
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Different Anti-Vaping Campaigns Attracting the Same Opponent Community
E-cigarettes (vape) are now the most commonly used tobacco product among youth in the United States. Ads are claiming e-cigarettes help smokers quit, but most of them contain nicotine, which can cause addiction and harm the developing adolescent brain. Therefore,... Read more
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Impedance and Magnetohydrodynamic Measurements for Label Free Detection and Differentiation of E. ColiandS. AureusUsing Magnetic Nanoparticles
In this paper, we used the distinguishable surface charge and mass of different bacterial strains for label free detection and differentiation of pathogen through impedance and magnetohydrodynamic analysis. For isolation of Escherichia coli and Staphylococcus aureus, functionalized magnetic nanoparticles (MNPs) were used. Proposed method is... Read more
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Guest Editorial IEEE BIBM 2017 Special Issue
Bioinformatics and biomedicine research is fundamental to our understanding of complex biological systems, impacting the science and technology of fields ranging from agricultural and environmental sciences to pharmaceutical and medical sciences. This type of research requires close collaboration among multidisciplinary... Read more
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Microaneurysm Detection Using Principal Component Analysis and Machine Learning Methods
Diabetic retinopathy (DR) is an eye abnormality caused by long-term diabetes and it is the most common cause of blindness before the age of 50. Microaneurysms (MAs), resulting from leakage from retinal blood vessels, are early indicators of DR. In... Read more
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MfeCNN: Mixture Feature Embedding Convolutional Neural Network for Data Mapping
Data mapping plays an important role in data integration and exchanges among institutions and organizations with different data standards. However, traditional rule-based approaches and machine learning methods fail to achieve satisfactory results for the data mapping problem. In this paper,... Read more
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A Novel Method to Predict Knee Osteoarthritis Progression on MRI Using Machine Learning Methods
This paper explored the hidden biomedical information from knee magnetic resonance (MR) images for osteoarthritis (OA) prediction. We have computed the cartilage damage index (CDI) information from 36 informative locations on tibiofemoral cartilage compartment from 3-D MR imaging and used... Read more
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State Estimation for Discrete Time-Delayed Genetic Regulatory Networks With Stochastic Noises Under the Round-Robin Protocols
This paper investigates the problem of state estimation for discrete time-delayed genetic regulatory networks with stochastic process noises and bounded exogenous disturbances under the Round-Robin (RR) protocols. The network measurement outputs obtained by two groups of sensors are transmitted to... Read more
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Anti-ISI Demodulation Scheme and Its Experiment-Based Evaluation for Diffusion-Based Molecular Communication
In diffusion-based molecular communication, the most common modulation technique is based on the concentration of information molecules. However, the random delay of molecules due to the channel with memory causes severe inter-symbol interference (ISI) among consecutive signals. In this paper,... Read more
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Development of an On-Chip Antibiotic Permeability Assay With Single Molecule Detection Capability
Electrophysiology is the method of choice to characterize membrane channels. In this paper, we demonstrate a patch pipette based simple miniaturization that allows performing conductance measurements on a planar lipid bilayer in a microfluidic channel. Membrane proteins were reconstituted into... Read more
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New Heights in 2017, Pushing on in 2018!
The IEEE Transactions on NanoBioscience thank its reviewers, editorial board members, and, most importantly, its authors and readers for their support in 2017 and wish them all the best for 2018! The Transactions reached new heights in 2017 with a record... Read more
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Adaptive Detection and ISI Mitigation for Mobile Molecular Communication
Current studies on modulation and detection schemes in molecular communication mainly focus on the scenarios with static transmitters and receivers. However, mobile molecular communication is needed in many envisioned applications, such as target tracking and drug delivery. Until now, investigations... Read more
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Maximum Likelihood Detection With Ligand Receptors for Diffusion-Based Molecular Communications in Internet of Bio-Nano Things
Molecular Communication (MC) is a bio-inspired communication technique that uses molecules as a method of information transfer among nanoscale devices. MC receiver is an essential component having profound impact on the communication system performance. However, the interaction of the receiver... Read more
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Axonal Channel Capacity in Neuro-Spike Communication
Novel nano-scale communication techniques are inspired by biological systems. Neuro-spike communication is an example of this communication paradigm which transfers vital information about external and internal conditions of the body through the nervous system. The analysis of this communication paradigm... Read more
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Special Section on Engineering Sciences in Biology and Medicine
ENGINEERING Sciences for Biology and Medicine (ESBM) is an exciting platform for researchers to discuss a wide range of modern biology and medicine goals. The third edition ESBM 2017 conference was organized by the Tunisian Association of Academic Researchers ATCU,... Read more
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A Bio-Inspired Hybrid Thermal Management Approach for 3-D Network-on-Chip Systems
3-D network-on-chip (NoC) systems are getting popular among the integrated circuit (IC) manufacturer because of reduced latency, heterogeneous integration of technologies on a single chip, high yield, and consumption of less interconnecting power. However, the addition of functional units in... Read more
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Photothermal Modeling and Analysis of Intrabody Terahertz Nanoscale Communication
Wireless communication among implanted nano-biosensors will enable transformative smart health monitoring and diagnosis systems. The state of the art of nano-electronics and nano-photonics points to the terahertz (THz) band (0.1–10 THz) and optical frequency bands (infrared, 30–400 THz, and visible,... Read more
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A New Adaptive Gamma Correction Based Algorithm Using DWT-SVD for Non-Contrast CT Image Enhancement
The performances of medical image processing techniques, in particular CT scans, are usually affected by poor contrast quality introduced by some medical imaging devices. This suggests the use of contrast enhancement methods as a solution to adjust the intensity distribution... Read more
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Classification of Schizophrenia Based on Individual Hierarchical Brain Networks Constructed From Structural MRI Images
With structural magnetic resonance imaging (MRI) images, conventional methods for the classification of schizophrenia (SCZ) and healthy control (HC) extract cortical thickness independently at different regions of interest (ROIs) without considering the correlation between these regions. In this paper, we... Read more
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Bacterial Relay for Energy-Efficient Molecular Communications
In multi-cellular organisms, molecular signaling spans multiple distance scales and is essential to tissue structure and functionality. Molecular communications is increasingly researched and developed as a key subsystem in the Internet-of-Nano-Things paradigm. While short range microscopic diffusion communications is well... Read more
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Transport of Liposome Encapsulated Drugs in Voxelized Computational Model of Human Brain Tumors
There are many obstacles in the transport of chemotherapeutic drugs to tumor cells that lead to irregular and non-uniform uptake of drugs inside tumors. The study of these transport problems will help with accurate prediction of drug transport and optimizing... Read more
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Terahertz Channel Model and Link Budget Analysis for Intrabody Nanoscale Communication
Nanosized devices operating inside the human body open up new prospects in the healthcare domain. Invivo wireless nanosensor networks (iWNSNs) will result in a plethora of applications ranging from intrabody health-monitoring to drug-delivery systems. With the development of miniature plasmonic... Read more
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Atomic Force Microscopy in Characterizing Cell Mechanics for Biomedical Applications: A Review
Cell mechanics is a novel label-free biomarker for indicating cell states and pathological changes. The advent of atomic force microscopy (AFM) provides a powerful tool for quantifying the mechanical properties of single living cells in aqueous conditions. The wide use... Read more
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A Fast Algorithm for Analysis of Molecular Communication in Artificial Synapse
In this paper, we analyze molecular communications (MCs) in a proposed artificial synapse (AS), whose main difference from biological synapses (BSs) is that it is closed, i.e., transmitter molecules cannot diffuse out from AS. Such a setup has both advantages... Read more
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IEEE BIBM 2016 Special Issue
Bioinformatics and biomedicine research is fundamental to our understanding of complex biological systems, impacting the science and technology of fields ranging from agricultural and environmental sciences to pharmaceutical and medical sciences. This type of research requires close collaboration among multidisciplinary... Read more
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Biomolecular Network Controllability With Drug Binding Information
Complex networks are ubiquitous in nature. In biological systems, biomolecules interact with each other to form so-called biomolecular networks, which determine the cellular behaviors of living organisms. Controlling the cellular behaviors by regulating certain biomolecules in the network is one... Read more
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FPGA Implementation of the Coupled Filtering Method and the Affine Warping Method
In ultrasound image analysis, the speckle tracking methods are widely applied to study the elasticity of body tissue. However, “feature-motion decorrelation” still remains as a challenge for the speckle tracking methods. Recently, a coupled filtering method and an affine warping... Read more
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Robust and Efficient Biomolecular Clustering of Tumor Based on p -Norm Singular Value Decomposition
High dimensionality has become a typical feature of biomolecular data. In this paper, a novel dimension reduction method named p-norm singular value decomposition (PSVD) is proposed to seek the low-rank approximation matrix to the biomolecular data. To enhance the robustness... Read more
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Detection of Glutathione by Glutathione-S-Transferase – Nanoconjugate Ensemble Electrochemical Device
This paper reports a novel electrochemical method for detection of Glutathione (GSH) using Glutathione-S-Transferase (GST) – ZnO composite nanoparticles to investigate the prospects of the method for detection of cancer at an early stage. The purified GST enzyme was bound... Read more
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PhosPred-RF: a novel sequence-based predictor for phosphorylation sites using sequential information only
Many recent efforts have been made for the development of machine learning based methods for fast and accurate phosphorylation site prediction. Currently, a majority of well-performing methods are based on hybrid information to build prediction models, such as evolutionary information,... Read more
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A Communication Theoretical Modeling of Axonal Propagation in Hippocampal Pyramidal Neurons
Understanding the fundamentals of communication among neurons, known as neuro-spike communication, leads to reach bio-inspired nanoscale communication paradigms. In this work, we focus on a part of neuro-spike communication, known as axonal transmission, and propose a realistic model for it.... Read more
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Modeling Contrast-Imaging-Assisted Optimal Targeted Drug Delivery: A Touchable Communication Channel Estimation and Waveform Design Perspective
To maximize the effect of treatment and minimize the adverse effect on patients, we propose to optimize nanorobots-assisted targeted drug delivery (TDD) for locoregional treatment of tumor from the perspective of touchable communication channel estimation and waveform design. The drug... Read more
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Abnormality Detection in Correlated Gaussian Molecular Nano-Networks: Design and Analysis
A nano-abnormality detection scheme (NADS) in molecular nano-networks is studied. This is motivated by the fact that early detection of diseases such as cancer plays a crucial role in their successful treatment. The proposed NADS is in fact a two-tier... Read more
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Use of Model Predictive Control and Artificial Neural Networks to Optimize the Ultrasonic Release of a Model Drug From Liposomes
The use of echogenic liposomes to deliver chemotherapeutic agents for cancer treatment has gained wide recognition in the last 20 years. Cancerous cells can develop multiple drug resistance (MDR), in part, due to the drop in concentration of chemotherapeutic agents... Read more
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Introduction to the Special Issue on Bioinformatics Research and Applications
This special issue includes a selection of papers presented at the 12th International Symposium on Bioinformatics Research and Application (ISBRA), which was held at Belorussian State University in Minsk, Belarus on June 5-8, 2016. The ISBRA symposium provides a forum... Read more
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A Framework for Integrating Multiple Biological Networks to Predict MicroRNA-Disease Associations
MicroRNAs have close relationship with human diseases. Therefore, identifying disease related MicroRNAs plays an important role in disease diagnosis, prognosis and therapy. However, designing an effective computational method which can make good use of various biological resources and correctly predict... Read more
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HapIso: An Accurate Method for the Haplotype- Specific Isoforms Reconstruction From Long Single-Molecule Reads
Sequencing of RNA provides the possibility to study an individual’s transcriptome landscape and determine allelic expression ratios. Single-molecule protocols generate multi-kilobase reads longer than most transcripts, allowing sequencing of complete haplotype isoforms. This allows partitioning the reads into two parental... Read more
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OVarCall: Bayesian Mutation Calling Method Utilizing Overlapping Paired-End Reads
Detection of somatic mutations from tumor and matched normal sequencing data has become a standard approach in cancer research. Although a number of mutation callers have been developed, it is still difficult to detect mutations with low-allele frequency even in... Read more
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Nanoparticles for siRNA-Based Gene Silencing in Tumor Therapy
Gene silencing through RNA interference (RNAi) has emerged as a potential strategy in manipulating cancer causing genes by complementary base-pairing mechanism. Small interfering RNA (siRNA) is an important RNAi tool that has found significant application in cancer therapy. However due... Read more
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An End-to-End Model of Plant Pheromone Channel for Long Range Molecular Communication
A new track in molecular communication is using pheromones which can scale up the range of diffusion-based communication from μ  meters to meters and enable new applications requiring long range. Pheromone communication is the emission of molecules in the air... Read more
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Performance Evaluation and Optimal Detection of Relay-Assisted Diffusion-Based Molecular Communication With Drift
In this paper, we consider a decode-and-forward (DF) relay-assisted diffusion-based molecular communication system inside one of the blood vessels of a human body with positive drift from transmitter to receiver. We use the normal approximation to the distribution of the... Read more
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Equivalent Discrete-Time Channel Modeling for Molecular Communication With Emphasize on an Absorbing Receiver
This paper introduces the equivalent discrete-time channel model (EDTCM) to the area of diffusion-based molecular communication (DBMC). Emphasis is on an absorbing receiver, which is based on the so-called first passage time concept. In the wireless communications community the EDTCM... Read more
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Onward and Upward!
THE IEEE TRANSACTIONS ON NANOBIOSCIENCE thank its reviewers, editorial board members, and most importantly its authors and readers for their support in 2016 and wishes them all the best for 2017! The Transactions had a year of consolidation, with the... Read more
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Optimal Fungal Space Searching Algorithms
Previous experiments have shown that fungi use an efficient natural algorithm for searching the space available for their growth in micro-confined networks, e.g., mazes. This natural “master” algorithm, which comprises two “slave” sub-algorithms, i.e., collision-induced branching and directional memory, has... Read more
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TargetM6A: Identifying N6-Methyladenosine Sites From RNA Sequences via Position-Specific Nucleotide Propensities and a Support Vector Machine
As one of the most ubiquitous post-transcriptional modifications of RNA, N6-methyladenosine ( m 6 A  ) plays an essential role in many vital biological processes. The identification of m 6 A  sites in RNAs is significantly important for both basic biomedical research and practical... Read more
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Comprehensive Reactive Receiver Modeling for Diffusive Molecular Communication Systems: Reversible Binding, Molecule Degradation, and Finite Number of Receptors
This paper studies the problem of receiver modeling in molecular communication systems. We consider the diffusive molecular communication channel between a transmitter nano-machine and a receiver nano-machine in a fluid environment. The information molecules released by the transmitter nano-machine into... Read more
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Analysis of Current Pulses in HeLa-Cell Permeabilization Due to High Voltage DC Corona Discharge
Corona discharges are commonly utilized for numerous practical applications, including bio-technological ones. The corona induced transfer of normally impermeant molecules into the interior of biological cells has recently been successfully demonstrated. The exact nature of the interaction of the corona... Read more
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Concentration-Encoded Subdiffusive Molecular Communication: Theory, Channel Characteristics, and Optimum Signal Detection
Unlike normal diffusion, in anomalous diffusion, the movement of a molecule is described by the correlated random walk model where the mean square displacement of a molecule depends on the power law of time. In molecular communication (MC), there are... Read more
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Block-Constraint Robust Principal Component Analysis and its Application to Integrated Analysis of TCGA Data
The Cancer Genome Atlas (TCGA) dataset provides us more opportunities to systematically and comprehensively learn some biological mechanism of cancers formation, growth and metastasis. Since TCGA dataset includes heterogeneous data, it is one of the bioinformatics bottlenecks to mine some... Read more
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Implementing Nonlinear Feedback Controllers Using DNA Strand Displacement Reactions
We show how an important class of nonlinear feedback controllers can be designed using idealized abstract chemical reactions and implemented via DNA strand displacement (DSD) reactions. Exploiting chemical reaction networks (CRNs) as a programming language for the design of complex... Read more
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Linear Channel Modeling and Error Analysis for Intra/Inter-Cellular Ca2+ Molecular Communication
The use of intra/inter-cellular calcium ion (Ca2+) signaling for molecular communication (MC) is investigated in this paper. In particular, the elevation of the intracellular Ca2+ concentration upon the external excitation, i.e., Ca2+ wave generation, and the intercellular propagation of Ca2+... Read more
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Ion Channel Based Bio-Synthetic Modulator for Diffusive Molecular Communication
In diffusion-based molecular communication (DMC), a transmitter nanomachine is responsible for signal modulation. Thereby, the transmitter has to be able to control the release of the signaling molecules employed for representing the transmitted information. In nature, an important class of... Read more
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IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2015 Special Issue
BIOINFORMATICS and biomedicine research is fundamental to our understanding of complex biological systems, impacting the science and technology of fields ranging from agricultural and environmental sciences to pharmaceutical and medical sciences. This type of research requires close collaboration among multidisciplinary... Read more
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Identifying Individual-Cancer-Related Genes by Re-balancing the Training Samples
The identification of individual-cancer-related genes typically is an imbalanced classification issue. The number of known cancer-related genes is far less than the number of all unknown genes, which makes it very hard to detect novel predictions from such imbalanced training... Read more
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Integrating Omics Data With a Multiplex Network-Based Approach for the Identification of Cancer Subtypes
Comprehensive characterization and identification of cancer subtypes have a number of applications and implications in life science and cancer research. Technologies centered on the integration of omics data hold great promise in this endeavor. This paper proposed a multiplex network-based... Read more
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Identification of DNA-Binding Proteins by Combining Auto-Cross Covariance Transformation and Ensemble Learning
DNA-binding proteins play a pivotal role in various intra- and extra-cellular activities ranging from DNA replication to gene expression control. With the rapid development of next generation of sequencing technique, the number of protein sequences is unprecedentedly increasing. Thus it... Read more
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Low-Complexity Adaptive Threshold Detection for Molecular Communication
This paper studies detection algorithms for diffusion-based molecular communication systems, where molecules freely diffuse as information carrier from a transmitter to a receiver in a fluid medium. The main limitations are strong intersymbol interference due to the random propagation of... Read more
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Molecular Communication Model for Targeted Drug Delivery in Multiple Disease Sites With Diversely Expressed Enzymes
Targeted drug delivery (TDD) for disease therapy using liposomes as nanocarriers has received extensive attention in the literature. The liposome’s ability to incorporate capabilities such as long circulation, stimuli responsiveness, and targeting characteristics, makes it a versatile nanocarrier. Timely drug... Read more
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Packet Fragmentation and Reassembly in Molecular Communication
This paper describes packet fragmentation and reassembly to achieve reliable molecular communication among bionanomachines. In the molecular communication described in this paper, a sender bionanomachine performs packet fragmentation, dividing a large molecular message into smaller pieces and embedding into smaller... Read more
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Introduction to the Special Issue on Bioinformatics
This Special Issue includes a selection of papers presented at the 11th International Symposium on Bioinformatics Research and Application (ISBRA), which was held at Old Dominion University in Norfolk, VA, USA, on May 7–10, 2015. The ISBRA symposium provides a... Read more
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Optimizing Associative Experimental Design for Protein Crystallization Screening
The goal of protein crystallization screening is the determination of the main factors of importance to crystallizing the protein under investigation. One of the major issues about determining these factors is that screening is often expanded to many hundreds or... Read more
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Genome-Wide Search for Translated Upstream Open Reading Frames in Arabidopsis Thaliana
Upstream open reading frames (uORFs) are open reading frames that occur within the 5′ UTR of an mRNA. uORFs have been found in many organisms. They play an important role in gene regulation, cell development, and in various metabolic processes.... Read more
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An Effective Approach for Glycan Structure De Novo Sequencing From HCD Spectra
Mass spectrometry has become a widely used analytical technique for proteomics study because of its high throughput and sensitivity. Among those applications, a specific one is to characterize glycan structure. Glycosylation is a frequently occurred post-translational modification of proteins which... Read more
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2014 Impact Factor: 2.3, 2015 Research Articles published: 100, 2016 Plan: En Avant!
The IEEE TRANSACTIONS ON NANOBIOSCIENCE thanks its reviewers, editorial board members, and most importantly its authors and readers for their support in 2015 and wishes them all the best for 2016! The Transactions experienced a 20% growth in submissions relative... Read more
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Low-Complexity Non-coherent Signal Detection for Nanoscale Molecular Communications
Nanoscale molecular communication is a viable way of exchanging information between nano-machines. In this investigation, a low-complexity and non-coherent signal detection technique is proposed to mitigate the inter-symbol-interference (ISI) and additive noise. In contrast to existing coherent detection methods of... Read more
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Kinesin-1 Expressed in Insect Cells Improves Microtubule in Vitro Gliding Performance, Long-Term Stability and Guiding Efficiency in Nanostructures
The cytoskeletal motor protein kinesin-1 has been successfully used for many nanotechnological applications. Most commonly, these applications use a gliding assay geometry where substrate-attached motor proteins propel microtubules along the surface. So far, this assay has only been shown to... Read more
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Intra-body Optical Channel Modeling for In-vivo Wireless Nanosensor Networks
In vivo wireless nanosensor networks (iWNSNs) consist of nanosized communicating devices, which can operate inside the human body in real time. iWNSNs are at the basis of transformative healthcare techniques, ranging from intra-body health-monitoring systems to drug-delivery applications. Plasmonic nanoantennas... Read more
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Introduction to the Special Section on the 8th International Conference on Nano/Molecular Medicine and Engineering (IEEE-NANOMED 2014)
This special Section of the IEEE TRANSACTIONS ON NANOBIOSCIENCE comprises 7 papers that are extended versions of accepted papers selected from the 8th International Conference on Nano/Molecular Medicine and Engineering (IEEE-NANOMED 2014). IEEE-NANOMED 2014 received 105 paper submissions, and every... Read more
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A Graphene and Aptamer Based Liquid Gated FET-Like Electrochemical Biosensor to Detect Adenosine Triphosphate
Here we report successful demonstration of a FET-like electrochemical nano-biosensor to accurately detect ultralow concentrations of adenosine triphosphate. As a 2D material, graphene is a promising candidate due to its large surface area, biocompatibility and demonstrated surface binding chemistries and... Read more
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A Molecular Communications Model for Drug Delivery
This paper considers the scenario of a targeted drug delivery system, which consists of deploying a number of biological nanomachines close to a biological target (e.g., a tumor), able to deliver drug molecules in the diseased area. Suitably located transmitters... Read more
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Centrifugal Filter Device for Detection of Rare Cells With Immuno-Binding
Many investigations have shown circulating tumor cells (CTCs) to serve as a significant biomarker of cancer progression and for cancer treatment. Multiple blood samples detection of CTCs during a course of treatment might facilitate a choice by a medical doctor... Read more
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Bio-inspired Nanonetworks for Targeted Cancer Drug Delivery
Biomimicry has been a great source of inspiration for many successful engineering solutions to date. Here, we propose to imitate several natural processes, some of which already occur within the human body, to construct bionanonetworks for targeted cancer drug delivery.... Read more
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Spatial Resolution Improvement of EEG Source Reconstruction using swLORETA
Electroencephalography (EEG) and Magnetic Resonance Imaging (MRI) are non invasive neuro-imaging modalities largely used in neurology explorations. MRI is considered as a static modality and could be so important for anatomy by its high spatial resolution. EEG, on the other... Read more
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3D silicon microstructures: a new tool for evaluating biological aggressiveness of tumour cells
In this work, silicon micromachined structures (SMS), consisting of arrays of 3-µm-thick silicon walls separated by 50-µm-deep, 5-µm-wide gaps, were applied to investigate the behaviour of eight tumour cell lines, with different origins and biological aggressiveness, in a three-dimensional (3D)... Read more
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Flexible Bioimpedance Sensor for Label-Free Detection of Cell Viability and Biomass
We introduce a flexible microfluidic bioimpedance sensor that is capable of detecting biomass and cell viability variations in a cell suspension. The sensor is developed on Indium Tin Oxide (ITO) coated Polyethylene terephthalate (PET) substrate and is devoid of gold,... Read more
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Introduction to the Special Section on Engineering Sciences for Biology and Medicine Conference (ESBM 2015)
This Special Section of the IEEE TRANSACTIONS ON NANOBIOSCIENCE comprises 9 accepted papers selected from the 2nd Engineering Sciences for Biology and Medicine Conference(ESBM 2015) organized in Tunisia from 1–3 May 2015. The conference received 52 contribution submissions from over... Read more
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D-MoSK Modulation in Molecular Communications
Molecular communication in nanonetworks is an emerging communication paradigm that uses molecules as information carriers. In molecule shift keying (MoSK), where different types of molecules are used for encoding, transmitter and receiver complexities increase as the modulation order increases. We... Read more
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An Acoustic Communication Technique of Nanorobot Swarms for Nanomedicine Applications
In this contribution, we present a communication paradigm among nanodevices, based on acoustic vibrations for medical applications. We consider a swarm of nanorobots able to communicate in a distributed and decentralized fashion, propelled in a biological environment (i.e., the human... Read more
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Nanoscale Surface Characterization of Human Erythrocytes by Atomic Force Microscopy: A Critical Review
Erythrocytes (red blood cells, RBCs), the most common type of blood cells in humans are well known for their ability in transporting oxygen to the whole body through hemoglobin. Alterations in their membrane skeletal proteins modify shape and mechanical properties... Read more
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Guest Editorial: IEEE International Conference on Bioinformatics and Biomedicine(BIBM2014)Special Issue
Bioinformatics and biomedicine research is fundamental to our understanding of complex biological systems, impacting the science and technology of fields ranging from agricultural and environmental sciences to pharmaceutical and medical sciences. This type of research requires close collaboration among multidisciplinary... Read more
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Clinical Documents Clustering Based on Medication/Symptom Names Using Multi-View Nonnegative Matrix Factorization
Clinical documents are rich free-text data sources containing valuable medication and symptom information, which have a great potential to improve health care. In this paper, we build an integrating system for extracting medication names and symptom names from clinical notes.... Read more
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Signal Quality Assessment Model for Wearable EEG Sensor on Prediction of Mental Stress
Electroencephalogram (EEG) plays an important role in E-healthcare systems, especially in the mental healthcare area, where constant and unobtrusive monitoring is desirable. In the context of OPTIMI project, a novel, low cost, and light weight wearable EEG sensor has been... Read more
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Identification Exon Skipping Events From High-Throughput RNA Sequencing Data
The emergence of next-generation high-throughput RNA sequencing (RNA-Seq) provides tremendous opportunities for researchers to analyze alternative splicing on a genome-wide scale. However, accurate identification of alternative splicing events from RNA-Seq data has remained an unresolved challenge in next-generation sequencing (NGS)... Read more
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Green Synthesis of Gold Nanoparticles by a Metal Resistant Arthrobacter nitroguajacolicus Isolated From Gold Mine
Biosynthesis of gold nanoparticles would benefit from the development of clean, nontoxic and environmentally acceptable procedures concerning microorganisms from bacteria to fungi and even algae. Actinobacteria are soil bacteria which have the enormous ability as biotechnological tools. In this paper,... Read more
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A Touch-Communication Framework for Drug Delivery Based on a Transient Microbot System
Recent progress in bioresorbable radio frequency electronics and engineered bacteria has promised the prospect of realizing a transient microbot (TM) system for therapeutic applications. The inorganic or organic miniature robots will dissolve into the human body after completing the required... Read more
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Simulation of the Dynamics of Bacterial Quorum Sensing
Quorum sensing (QS) is a signaling mechanism that pathogenic bacteria use to communicate and synchronize the production of exofactors to attack their hosts. Understanding and controlling QS is an important step towards a possible solution to the growing problem of... Read more
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Nanowire-Imposed Geometrical Control in Studies of Actomyosin Motor Function
Recently, molecular motor gliding assays with actin and myosin from muscle have been realized on semiconductor nanowires coated with Al2O3. This opens for unique nanotechnological applications and novel fundamental studies of actomyosin motor function. Here, we provide a comparison of... Read more
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Microfluidic-Assisted Fabrication of Flexible and Location Traceable Organo-Motor
In this paper, we fabricate a flexible and location traceable micro-motor, named organo-motor, assisted by microfluidic devices and with high throughput. The organo-motors are composed of organic hydrogel material, poly (ethylene glycol) diacrylate (PEGDA), which can provide the flexibility of... Read more
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Guest Editorial: Special Issue Micro- and Nanomachines
The world of artificial micro- and nanomachines has greatly expanded over the last few years to include a range of disciplines from chemistry, physics, biology, to micro/nanoengineering, robotics, and theoretical physics. The dream of engineering nanomachines involves fabricating devices that... Read more
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Guest Editorial : Introduction to the Special Issue on the 10th International Symposium on Bioinformatics Research and Applications (ISBRA 2014)
THIS SPECIAL Issue of the IEEE TRANSACTIONS ON NANOBIOSCIENCE comprises 11 papers that are extended versions of accepted papers selected from the 10th International Symposium on Bioinformatics Research and Applications (ISBRA 2014). ISBRA 2014 received 119 full paper submissions from... Read more
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A Generalized dSpliceType Framework to Detect Differential Splicing and Differential Expression Events Using RNA-Seq
ACCESS PAPER DATA READ FULL ARTICLE ON IEEE XPLORE Abstract Transcriptomes are routinely compared in term of a list of differentially expressed genes followed by functional enrichment analysis. Due to the technology limitations of microarray, the molecular mechanisms of differential expression is poorly... Read more
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Heterogeneous Network Model to Infer Human Disease-Long Intergenic Non-Coding RNA Associations
ACCESS PAPER DATA READ FULL ARTICLE ON IEEE XPLORE Abstract With the knowledge of molecular biology it is highlighting that long non-coding RNAs (lncRNAs) play a critical role in many important biological processes, such as imprinting control, cell differentiation, immune responses, human diseases,... Read more
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Error Performance of Diffusion-Based Molecular Communication Using Pulse-Based Modulation
ACCESS PAPER DATA READ FULL ARTICLE ON IEEE XPLORE Abstract Diffusion-based molecular communication (DMC) is a promising technique for nanonetworks. The main objective of this paper is to evaluate the error performance of DMC employing pulse-based modulation scheme. We derive closed-form expressions for... Read more
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RANWAR: Rank-Based Weighted Association Rule Mining From Gene Expression and Methylation Data
ACCESS PAPER DATA READ FULL ARTICLE ON IEEE XPLORE Abstract Ranking of association rules is currently an interesting topic in data mining and bioinformatics. The huge number of evolved rules of items (or, genes) by association rule mining (ARM) algorithms makes confusion to... Read more
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Synthesis of ZnO Nanosphere for Picomolar Level Detection of Bovine Serum Albumin
ACCESS PAPER DATA READ FULL ARTICLE ON IEEE XPLORE Abstract In this paper, we demonstrate an electrical detection technique based on solution processed zinc oxide nanosphere for ultra-low level detection of bovine serum albumin (BSA). Our sensor device works on the basis of... Read more
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Editorial: 1000 Issues and 1,000 Pages of Interdisciplinary Research Advances in 2015!
ACCESS PAPER DATA READ FULL ARTICLE ON IEEE XPLORE Abstract The IEEE transactions on nanobioscience thank its reviewers, editorial board members, and most importantly its authors and readers for their support in 2014 and look forward to serving them even better in 2015!  The... Read more
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Fungus-Mediated Synthesis of Gold Nanoparticles and Standardization of Parameters for its Biosynthesis
ACCESS PAPER DATA READ FULL ARTICLE ON IEEE XPLORE 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 (1 mM), as nanoparticles... Read more
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Theoretical Modelling and Experimental Validation of Surface Stress in Thrombin Aptasensor
ACCESS PAPER DATA READ FULL ARTICLE ON IEEE XPLORE Abstract Adsorption of target molecules on the immobilized microcantilever surface produced beam displacement due to the differential surface stress generated between the immobilized and non-immobilized surface. Surface stress is caused by the intermolecular forces... Read more
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Intravenously Administered gamma-Ferric Oxide Particle Amount Measured Using Vibrating Sample Magnetometer
ACCESS PAPER DATA READ FULL ARTICLE ON IEEE XPLORE Abstract Dispersions of platelet gamma-ferric oxide particles 30–50nm in size were intravenously administered to mice and the amount of particles accumulated in each tissue was obtained by magnetization measurement using a vibrating sample magnetometer.... Read more
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Cytotoxic Effects of PLGA Coated Iron Oxide Nanoparticles
ACCESS PAPER DATA READ FULL ARTICLE ON IEEE XPLORE Abstract The purpose of this study was to investigate the uptake and cytotoxic effects of magnetic poly lactic-co-glycolic acid (PLGA)-coated iron oxide nanoparticles as a carrier of 5-fluorouracil (5-FU) and X-ray on the level... Read more