Genes in an organism's DNA (genome) have embedded them information about proteins, which are the molecules that do most of a cell's work. A typical bacterial genome contains on order 5,000 genes. Mammalian genomes can contain tens thousands For each sequenced, challenge is to identify protein components (proteome) being actively used for given set conditions. Fundamentally, sequence alignment matching problem focused unlocking genetic code, making it possible assemble "tree life" by...

Abstract Motivation: The standard approach to identifying peptides based on accurate mass and elution time (AMT) compares profiles obtained from a high resolution spectrometer database of previously identified tandem spectrometry (MS/MS) studies. It would be advantageous, with respect both accuracy cost, only search for those that are detectable by MS (proteotypic). Results: We present support vector machine (SVM) model uses simple descriptor space 35 properties amino acid content, charge,...

The dengue viruses (DENVs) exist as numerous genetic strains that are grouped into four antigenically distinct serotypes. DENV from each serotype can cause severe disease and threaten public health in tropical subtropical regions worldwide. No licensed antiviral agent to treat infections is currently available, there an acute need for the development of novel therapeutics. We found a synthetic small interfering RNA (siRNA) (DC-3) targeting highly conserved 5' cyclization sequence (5'CS)...

Abstract Motivation: As the amount of biological sequence data continues to grow exponentially we face increasing challenge assigning function this enormous molecular ‘parts list’. The most popular approaches make use simplifying assumption that similar functional molecules, or proteins, sometimes have composition, sequence. However, these algorithms often fail identify remote homologs (proteins with but dissimilar sequence) which are a significant fraction total homolog collection for given...

The standard approach to identifying peptides based on accurate mass and elution time (AMT) compares profiles obtained from a high resolution spectrometer database of previously identified tandem spectrometry (MS/MS) studies. It would be advantageous, with respect both accuracy cost, only search for those that are detectable by MS (proteotypic).We present support vector machine (SVM) model uses simple descriptor space 35 properties amino acid content, charge, hydrophilicity polarity the...

Abstract Motivation: BLAST remains one of the most widely used tools in computational biology. The rate at which new sequence data is available continues to grow exponentially, driving emergence fields biological research. At same time, multicore systems and conventional clusters are more accessible. ScalaBLAST has been designed run on multiprocessor with an eye extreme parallelism, enabling parallel calculations using >16 000 processing cores a portable, robust, fault-resilient...

Progress in modern biology is being driven, part, by the large amounts of freely available data public resources such as International Nucleotide Sequence Database Collaboration (INSDC), world's primary database biological sequence (and related) information. INSDC and similar databases have dramatically increased pace fundamental discovery enabled a host innovative therapeutic, diagnostic, forensic applications. However, high-value, openly shared with high degree assumed trust, these...

We evaluate statistical models used in two-hypothesis tests for identifying peptides from tandem mass spectrometry data. The null hypothesis H0, that a peptide matches spectrum by chance, requires information on the probability of by-chance between fragments and peaks spectrum. Likewise, alternate HA, is due to particular peptide, probabilities would indeed be observed if it was causative agent. compare these determining identification rates produced using an independent data set. initial...

Systems biology attempts to reconcile large amounts of disparate data with existing knowledge provide models functioning biological systems. The cyanobacterium Cyanothece sp. ATCC 51142 is an excellent candidate for such systems studies because: (i) it displays tight functional regulation between photosynthesis and nitrogen fixation; (ii) has robust cyclic patterns at the genetic, protein metabolomic levels; (iii) potential applications bioenergy production carbon sequestration. We have...

The challenge of remote homology detection is that many evolutionarily related sequences have very little similarity at the amino acid level. Kernel-based discriminative methods, such as support vector machines (SVMs), use representations derived from sequence properties been shown to superior accuracy when compared traditional approaches for task detection.We introduce a new method feature representation based on physicochemical primary protein sequence. A distribution property scores are...

Infrastructure Distributed Denial of Service (IDDoS) attacks continue to be one the most devastating challenges facing cyber systems. The new generation IDDoS exploits inherent weakness infrastructure, including deterministic nature routing, skewed distribution flows, and Internet ossification discover network critical links launch highly stealthy flooding that are not observable at victim’s end. In this paper, first, we propose a metric quantitatively measure potential susceptibility any...

The deterministic nature of existing routing protocols has resulted into an ossified Internet with static and predictable network routes. This gives persistent attackers (e.g. eavesdroppers DDoS attackers) plenty time to study the identify vulnerable (critical) links plan devastating stealthy attacks. Recently, Moving Target Defense (MTD) based approaches have been proposed defend against DoS However, MTD for route mutation are oriented towards re-configuring parameters in Local Area...

Cyber entities in many ways mimic the behavior of organic systems. Individuals or groups compete for limited resources using a variety strategies, most effective which are reused and refined later 'generations'. Traditionally this has made detection malicious very difficult because 1) recognition systems often built on exact matching to pattern that can only be 'learned' after entity reveals itself 2) enormous volume variation benign is an overwhelming source previously unseen confound...

Role of I Kr in Rabbit Sinoatrial Node. Introduction: A rapidly activating delayed rectifier potassium current (I ) is known to have an important role determining the properties spontaneous pacing enzymatically isolated rabbit sinoatrial node (SAN) cells. The functional characteristics are conferred by its dependence on time, voltage, and external potassium. aim this study was develop a rigorous mathematical representation for based experimental findings investigate automaticity...

One of the biggest challenges faced by cyber defenders is that attacks evolve more rapidly than our ability to recognize them. We propose a moving target defense concept in which means detection set motion. This done away from static signature-based and instead adopting biological modeling techniques describe families related sequences. present here one example for how apply evolutionary models sequences, demonstrate feasibility this technique on analysis complex, evolving software project....

Mass spectrometry (MS)-based proteomics is a powerful and popular high-throughput process for characterizing the global protein content of sample. In shotgun proteomics, typically proteins are digested into fragments (peptides) prior to mass analysis, presence in inferred from identification its constituent peptides. Thus, accurate proteome characterization dependent upon accuracy this peptide step. Database search routines generate predicted spectra all peptides derived known genome...

Natural multi-agent systems often rely on "correlated random walks" (random walks that are biased toward a current heading) to distribute their agents over space (e.g., for foraging, search, etc.) Our contribution involves creation of new movement and pheromone model applies the concept heading bias in multi-agent, digital-ants system designed cyber-security monitoring. We examine relative performance effects both speed discovery target search-area coverage two-dimensional network layout....

The cyber environment has rapidly evolved from a curiosity to an essential component of the contemporary world. As expanded and become more complex, so have nature adversaries styles attacks. Today, incidents are expected part life. result, cybersecurity research emerged address adversarial attacks interfering with or preventing normal activities. Historical response is heavily skewed tactical responses emphasis on rapid recovery. While threat mitigation important can be time critical,...

One essential component of resilient cyber applications is the ability to detect adversaries and protect systems with same flexibility will use achieve their goals. Current detection techniques do not enable this degree because most existing are built using exact or regular-expression matching libraries rule sets. Further, network traffic defies traditional security approaches that focus on limiting access based passwords examination lists installed downloaded programs. These readily apply...

Many phenomena that we wish to discover are comprised of sequences events or event primitives. Often signatures constructed identify such using either distributions frequencies attributes, specific subsequences known correlate the phenomena. Distribution-based identification does not capture essence sequence behaviors and therefore may suffer from lack specificity. At other extreme, target is often too suffers lower sensitivity when natural variations arise in phenomena, measuring process,...

In production multi-user high-performance (HPC) batch computing environments, wait times for scheduled jobs are highly dynamic. For scientific users, the primary measure of efficiency is wall clock time-to-solution. high throughput applications, such as many kinds biological analysis, computational work to be done can flexibly taking a longer time on small number processors or shorter large processors. Therefore capability choose platform at run-time based both processing capabilities and...