In all fields of molecular biology, researchers are increasingly challenged by experiments planned and evaluated on the basis of nucleic acid and protein sequence data generally retrieved from public databases. Despite the wide spectrum of available Web-based software tools for sequence analysis, the routine use of these tools has disadvantages, particularly because of the elaborate and heterog...

The concept of hairpin structures in formal languages is motivated from the biocomputing and bioinformatics fields. Hairpin (-free) DNA structures have numerous applications to DNA computing and molecular genetics in general. A word is called hairpin-free if it cannot be written in the form , with certain additional conditions, for an involution (a function with the property that equals the ide...

Within the last 25 years, bacteriophage integrases have rapidly risen to prominence as genetic tools for a wide range of applications from basic cloning to genome engineering. Serine integrases such as that from ϕC31 and its relatives have found an especially wide range of applications within diverse micro-organisms right through to multi-cellular eukaryotes. Here, we review the mechanisms of t...

The major goal of precision medicine is to improve human health. A feature that unites much research in the field is the use of large datasets such as genomic data and electronic health records. Research in this field includes examination of variation in the core bases of DNA and their methylation status, through variations in metabolic and signaling molecules, all the way up to broader systems...

One of the challenges in biocomputing is to enable the efficient use of a wide variety of rapidly evolving computational methods to simulate, analyze and understand the complex interactions of molecular systems. Our laboratory investigates several areas including molecular visualization, protein-ligand docking, protein-protein docking, molecular surfaces and the derivation of phenomenological p...

The present study aims at integrating drug-releasing materials with signal-processing biocomputing systems. Enzymes alanine transaminase (ALT) and aspartate transaminase (AST)—biomarkers for liver injury—were logically processed by a biocatalytic cascade realizing Boolean AND gate. Citrate produced in the system was used to trigger a drugmimicking release from alginate microspheres. In order to...

We consider flow systems that have been utilized for small-scale biomolecular computing and digital signal processing in binary-operating biosensors. Signal measurement is optimized by designing a flow-reversal cuvette and analyzing the experimental data to theoretically extract the pulse shape, as well as reveal the level of noise it possesses. Noise reduction is then carried out numerically. ...

In this paper, we describe our system for detecting adverse reactions from tweets, a task organized as part of Pacific Symposium of Biocomputing Social Media Mining Shared Task. The shared task primarily involves a binary classification of the tweets, whether they contain description of adverse drug reaction or not. We propose an ensemble machine learning classifier to tackle the unbalanced dis...

Processes involving multi-input multi-step reaction cascades are used in developing novel biosensing, biocomputing, and decision making systems. In various applications different changes in responses of the constituent processing steps (reactions) in a cascade are desirable in order to allow control of the system’s response. Here we consider conversion of convex response to sigmoid by “intensit...

ABTRACT: We developed and experimentally verified an analytical model to describe diffusion of oligonucleotides from stable hydrogel beads. The synthesized alginate beads are Fe-cross-linked as well as polyelectrolyte-doped for uniformity and stability at physiological pH. Data on diffusion of oligonucleotides from inside the beads provide physical insights into the volume nature of the immobil...