ENGINEERING RESEARCH PAPERS

bioinformatics 2016 IEEE PAPER




An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics
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This talk will present an overview of Apache Hadoop and associated open source software projects. Current Hadoop usage within the bioinformatics community will be summarized, and the advantages of Hadoop will be discussed as they Aims and Scope The Book Series in Translational Bioinformatics is a powerful and integrative resource for understanding and translating discoveries and advances of genomic, transcriptomic, proteomic and bioinformatic technologies into the study of human

Microarray-based Functional Nanoproteomics for an Industrial Approach to Cancer: I Bioinformatics and miRNAome
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Abstract Oral Lichen Planus (OLP) is a common chronic inflammatory disease, which involves the mucous membranes of the oral cavity, with an overall agestandardized prevalence of 1.27%(0.96% in men and 1.57% in women) as reported in the literature by

Multiple Sequence Alignment of Model Plants Using Bioinformatics Approach
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Abstract–Bioinformatics is an interdisciplinary area of research, which also plays a vital role in the field of agriculture based studies. Tools of bioinformatics provides significant role in agriculture research. Present paper is also focusing on agriculture informatics. As we

Bioinformatics analysis of differentially expressed miRNAs in plasma of respiratory distress syndrome
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Abstract: Purpose: This study was aimed to reveal the involvement of miRNAs in RDS by bioinformatics analysis. Methods: The data in this study came from the paper of Kan et al. who analyzed the microRNA (miRNA) expression profile between RDS patients and

Bioinformatics investigation of therapeutic mechanisms of Xuesaitong capsule treating ischemic cerebrovascular rat model with comparative transcriptome
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Abstract: Background: Xuesaitong soft capsule (XST) which consists of panax notoginseng saponin (PNS) has been used to treat ischemic cerebrovascular diseases in China. The therapeutic mechanism of XST has not been elucidated yet from prospective of genomics

The largest distributed network of bioinformatics centres in the world: Biotechnology Information System Network
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Following the bioinformatics policy document, the recent years have seen the nurturing of the North Eastern Bioinformatics Network and also international collaborative ventures with countries in Asia and Europe. The trend of an admixture of experimental and

Bioinformatics Applications in Life Sciences and Technologies
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Life sciences researchers collect and analyze a high amount of different types of scientific data, including DNA, RNA and amino acid sequences, in-situ and microarray gene expression data, protein structures and biological pathways, as well as biological signals

Obesity-Related Genes and Oral Cancer: A Bioinformatics Approach and Systematic Review
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Abstract It is important to understand the biological processes linking obesity and cancer to targets for development of better therapeutic strategies. This study aims to synthesize knowledge regarding possible associations between obesity-related

of microRNA-23b-3p down-regulation with progression and survival in pancreatic duct adenocarcinoma and its prospective function via bioinformaticsanalysis
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Abstract: Background: MicroRNAs (miRNAs) have been reported in various human malignancies, which play important roles in tumorigenesis and progression, acting as oncogenes or tumor suppressors. However, the role of miR-23b-3p in pancreatic duct

Bioinformatics-based design of novel antigenic B-cell linear epitopes of Deinagkistrodon acutus venom
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Abstract.–OBJECTIVE: With the help of bioin-formatics analysis, we wished to develop a novel antivenom against the Deinagkistrodon (D.) acutus snake venom using B-cell linear epitopes of three primary toxins (serine protease, metalloprotease, and phospholipase A2

Application of Data Mining in Bioinformatics
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Abstract: This article highlights some of the basic concepts of bioinformatics and data mining. The major research areas of bioinformatics are highlighted. The application of data mining in the domain of bioinformatics is explained. It also highlights some of the current

Homology Modelling, Bioinformatics Analysis and Insilico Functional Annotation of an Antitoxin Protein from Streptomyces coelicolor A3 (2)
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Abstract Streptomyces coelicolor A3 (2) is a soil-dwelling, filamentous bacteria and a reservoir of a wide range of natural antibiotics. A hypothetical protein SCO2235 of this bacterium, comprising of 87 residues was selected for in silico analysis. Numerous

Multiple Sequence Alignment of Model Plants Using Bioinformatics Approach
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Abstract–Bioinformatics is an interdisciplinary area of research, which also plays a vital role in the field of agriculture based studies. Tools of bioinformatics provides significant role in agriculture research. Present paper is also focusing on agriculture informatics. As we Biological and biomedical research are increasingly driven by experimental techniques that challenge our ability to analyse, process and extract meaningful knowledge from the underlying data. The impressive capabilities of next generation sequencing technologies,

Identification potential biomarkers and therapeutic agents in multiple myeloma based on bioinformatics analysis
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RESULTS: A total of 573 DEGs were identified in MM samples comparing with normal samples, including 322 down- and 251 up-regulated genes. The DEGs were separated into two clus- ters. Down-regulated genes were mainly en- riched in cell cycle function, while up-

Engineering lhRNA based molecule to interfere replication of dengue virus in transgenic Aedes aegypti mosquitoes: Bioinformatics approach
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Abstract As a preliminary step towards the development of transgenic Aedes aegypti mosquito's resistance to Sri Lankan dengue viruses (SLDENV), the identification of previously unpublished DNA sequence of the construct, AeCPA/Mnp+/i/Mnp-/svA, was

Identification of drug sensitive gene motifs using epigenetic profiles derived from bioinformatics databases
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My deep gratitude first goes to Dr. Karen Katula who guided, counselled, and challenged me through my research and coursework. Having worked with her for the last 4 years, Dr. Katula has taught me not only how to perform science, but also how to ask the important

Big Data Analytics: Bioinformatics Perspective
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Abstract-In current digital era, every experimental instruments, clinical system, laboratory apparatuses are embedded with digital devices, due to the digitization of research and experimental processes, biological databases has increased in volume tremendously.

Big Genomic Data in Bioinformatics Cloud
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Abstract The achievement of Human Genome project has led to the proliferation of genomic sequencing data. This along with the next generation sequencing has helped to reduce the cost of sequencing, which has further increased the demand of analysis of this large

Genomic Databases and Softwares: In Pursuit of Biological Relevance throughBioinformatics
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Abstract With the completion of human genome project, a plethora of information had been available for exploring various unanswered questions related to cell and molecular biology. Bioinformatics has been instrumental in unravelling the genetic, phenotypic, structural and

BIOINF525: INTRODUCTION TO BIOINFORMATICS LAB SESSION 3
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Protein Structure Visualization and Small Molecule Docking http://bioboot.github.io/bioinf525_w16 /module1/#1.3 Dr. Barry Grant Jan 2016 Section 1: Introduction to the RCSB Protein Data Bank (PDB) The PDB archive is the major repository of information about the 3D

BioGraphDB: a new GraphDB collecting heterogeneous data forbioinformatics analysis
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Abstract:Current bioinformatics databases provide huge amounts of different biological entities such as genes, proteins, diseases, microRNA, annotations, literature references. In many case studies, a bioinformatician often needs more than one type of resource in order

Architecture exploration of FPGA based accelerators for bioinformaticsapplications
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Rapid advances in VLSI technology have enabled fabrication of billions of transistors on a single chip. Technology scaling has allowed more than one processor core to be integrated in a single chip. The current computing systems, including desktops, laptops, and mobile

Structure Prediction of Mutant Proteins Responsible for Certain Genetic Disorders Using Bioinformatics Tools
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Abstract: In order to understand real cause behind any disease it is very important to understand molecular basis of life and what type of molecular mechanisms are involve behind diseases. We can easily understand molecular basis of life if we are able to know

The Value and Impact of the European Bioinformatics Institute
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The European Bioinformatics Institute (EMBL-EBI), located on the Wellcome Genome Campus in Hinxton, UK, manages public life science data on a very large scale, making a rich resource of information freely available to the global life science community. EMBL-

Bioinformatics for RNA-Seq Data Analysis
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Abstract While RNA sequencing (RNA-seq) has become increasingly popular for transcrip- tome profiling, the analysis of the massive amount of data generated by large-scale RNA- seq still remains a challenge. RNA-seq data analyses typically consist of (1) accurate

Identification of key genes associated with idiopathic pulmonary fibrosis usingbioinformatics analysis
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Abstract: Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal interstitial lung disease. The goal of this study is to elucidate the molecular mechanism of IPF. GSE24206 was downloaded from Gene Expression Omnibus, which included 17 IPF and 6 control

Multiple Sequence Alignmen Bioinformatics
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Abstract–Bioinformatics is an interdisciplinary research, which also plays a vital role in the f agriculture based studies. Tools of bioinformatics p significant role in agriculture research. Present paper focusing on agriculture informatics. As we know bioinformatics tool we can

Bioinformatics Tools for Protein Analysis
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ABSTRACT Understanding of the relationship between amino acid sequence and three dimensional structure of protein is one of the main objects of bioinformatics, if the relationship is known; it can be helpful for prediction of the protein structure from its amino

Bioinformatics Analysis of Evolution of Secondary Structures of Protein Trypsin Beta
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ABSTRACT Impact of divergence of amino acid sequences of protein during evolution on the secondary structures of polypeptide and phylogenetic significance of different secondary structures such as alpha helix, beta sheet and random coil in evolution are not known.

GENERALIZED SPECTRAL-ANALYTICAL METHOD FOR BIOMEDICAL ANDBIOINFORMATICS DATA PROCESSING
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As a result of this procedure, the transition is made from a point-wise signal recording to its spectral representation. All further analysis and processing operations are performed over the spectrum. Proposed technique is adaptive to the class of signals. It consists in

Novel insights into the structural mechanisms of FexB protein resistance towards Chloramphenicol: a bioinformatics approach
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ABSTRACT Chloramphenicol (Clm) is one of the most widely used broad spectrum antibiotic in veterinary medicine. Recent studies have shown that there is a development of an acquired resistance against Clm by FexB protein which is encoded by its fexB phenicol Abstract The expression in silico, which means performed on computer or via computer simulation, has been seen with increasing frequency, in almost every area of knowledge, in scientific papers published in the last few years. This is particularly true with regard to

BIOINFORMATICS ADVANCES IN GENOMICS–A REVIEW
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Summary Genomics is a discipline in genetics that applies recombinant DNA technology, DNA sequencing methods and bioinformatics to sequence, assemble and analyze the function and structure of genome, the complete set of DNA within a single cell of an

Comprehensive Analysis of rsSNPs Associated with Hypertension Using In-Silico Bioinformatics Tools
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Abstract Genetic epidemiological studies have suggested that several genetic variants increase the risk for hypertension. It is likely that a number of genes rather than a single gene account for the heritability of this complex disorder. However, the genetic analysis of

The Role of Intellectual Property in Bioinformatics in Bulgaria
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Abstract Intellectual Property (IP) rights are essential and very important in today's technology-driven world. In fact IP is directly related to the information, which contains in the objects themselves. In other words, the IP is the ownership of the information, which This proceedings volume contains papers presented at the 16th Workshop on Algorithms in Bioinformatics (WABI 2016) that was held at Aarhus University, Aarhus, Denmark, August 22– 24, 2016. WABI 2016 was one of eight conferences that were organized as part of ALGO

Bioinformatics-Its Challenges
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Abstract: Bioinformatics is a new science that is glowing out in the recent years. It is a multidisciplinary science that is made out of different kinds of other scientific fields like biology, computer science, chemistry, statistics, mathematics and others. Bioinformatics as

Application of Bioinformatics in the Study of Type 1 Diabetes
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ABSTRACT Single nucleotide polymorphism (SNP) that occurs in an experimentally detected binding site, and is closely linked with a disease associated SNP, is more likely to play a biological role in the genome than other SNPs that occur in parts for which there is

Iore Journal of Bioinformatics Computational Biology
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Abstract Educational neuroscience is an innovative scientific field which combines among others the Neuroscience, Cognitive Science and Educational Psychology, suggesting the observation of brain function in order to improve the learning and educational process.

A GRID-based multilayer architecture for bioinformatics
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Abstract. The volume and complexity of biological data and informations available today need a significant computational data and processes analysis. A huge amount of bioinformatics databases and tools is available. Some of them allow bioinformaticians to

TRANSLATIONAL BIOINFORMATICS FOR MASS SPECTROMETRY IMAGING IN CLINICAL RE-SEARCH SETTINGS
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Cancer incidence in Europe was recently estimated at 3.45 million cases, with 1.75 million deaths, and costing the EU 124 billion Euros every year. With such incidence rates, fundamental understanding of cancer biology is required to prevent (prognosis), identify (

Bioinformatics around next generation sequencing
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Abstract Next generation sequencing (NGS) is revolutionizing biological research. Genomic projects that until recently could only be realised with multi-million dollar budgets are now within the reach of even small research groups. It is almost trivial to generate large

Bioinformatics Analysis of Main Cis-elements in Oxidative Defense Pathway Genes of Oryza sativa plant
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Abstract The survey of promoters structure in genes of oxidative defense biochemically pathway for Oryza sativa forms the aim of this research. We found genes response to aspect co-expression relationships against to environmental conditions. it is proposed that which

Sampling Random Bioinformatics Puzzles using Adaptive Probability Distributions
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Abstract. We present a probabilistic logic program to generate an educational puzzle that introduces the basic principles of next generation sequencing, gene finding and the translation of genes to proteins following the central dogma in biology. In the puzzle, a

Improving bioinformatics analysis of large sequence datasets parallelizing tools for population genomics
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Abstract. Next-generation sequencing (NGS) technologies initiated a revolution in genomics, producing massive amounts of biological data and the consequent need for adapting current computing infrastructures. Multiple alignment of genomes, analysis of variants or

Drug Reviews using Opinion Mining and Fuzzy Modeling for BioinformaticsApplications
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Abstract: Online reviews, blogs, discussion forums on chronic diseases and drugs are excellent supporting resources for patients. Extracting information from these substantial bodies of texts is challenging issue. For this purpose, in this research investigated Fuzzy

Bioinformatics informations for Constructed Mammalian expression vector using nested PCR technique
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Abstract: Present study aims to used virtual design to transfer cytomegalovirus premotor (CMV) and red fluorescence protein gene (RFP) to mammalian expression vector by nested PCR technique, free bioinformatics soft wear were used to design primers, linkers and

Evolving Graph Compression using Similarity Measures for BioinformaticsApplications
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Abstract:Many real-world graphs, including those storing various forms of biological data, are of such large size that storing and processing their information has too high a cost. As a result, one possible solution is to compress the graphs by merging nodes into supernodes

Evolution of Bioinformatics Principal and Practices
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Abstract:Bioinformatics is another and fast developing area that is rising up out of the fields of sub atomic science or we can say experimental molecular biology biochemistry. It coordinates numerous center subjects like Biology, Computer science, Software

target EBOLA VIRUS WITH CURCUMIN
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1ICAR-Indian Institute of Vegetable Research, PB No. 01, PO Jakhini (Shahanshapur), Varanasi-221305 (UP) India, E-mail: suhaskarkute@ gmail. com and 2Bioinformatics, MMV, Banaras Hindu University, Varanasi-221005 (UP) India hytochemicals found in most of the

ETLs for importing UniProtKB, HGNC, and Reactome into a bioinformaticsgraph database
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Consiglio Nazionale delle Ricerche, Istituto di Calcolo e Reti ad Alte Prestazioni (ICAR) – Sede di Cosenza, Via P. Bucci 41C, 87036 Rende, Italy, URL: www.icar.cnr.it – Sede di Napoli, Via P. Castellino 111, 80131 Napoli, URL: www.na.icar.cnr.it – Sede di Palermo, Viale delle

Juan B. Gutierrez, Ph. D. Assistant Professor, Department of Mathematics, Institute of Bioinformatics University of Georgia 200 DW Brooks Dr, Athens, GA 30602
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I am interested in PDEs, ODEs, computational mathematics, bioinformatics, and pattern classification. I explore mathematical and computational models that connect genes to ecology. My current direction of research includes:(i) integration of multiple omic

Bioinformatics: Benefits to Mankind
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Abstract: The storage and analysis of biological data using certain algorithms and computer softwares is called bioinformatics. The applications that bioinformatics offer to the civilized world are more than just being a researcher's tool for structural and functional analysis.

Characterization of Heat-Responsive Transcription Factor under Heat Stress in Wheat Triticumaestivum L Using Bioinformatics Tools
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ABSTRACT: Heat stress is one of the major problems in wheat growth and yield. It affects the growth and development of plant by causing denaturation of various enzymes, defunct pollen, and pseudo seed setting problem which ultimately affect the productivity. Wheat,

Integrating Scientific Workflows with Scientific Gateways: A BioinformaticsExperiment in the Brazilian National High-Performance Computing Network
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Abstract. Bioinformatics experiments are rapidly and constantly evolving due improvements in sequencing technologies. These experiments usually demand high performance computation and produce huge quantities of data. They also require different programs to

Subject name Bioinformatics Subject code E. 1. BIOI. SC. ECTIE. B Department Department of Genetics, Plant Breeding and Seed Science Faculty Faculty of
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This course is designed to introduce students to the current bioinformatics algorithms/concepts and their implementations. The course objectives: teach students cast a molecular biology problem as a bioinformatic problem, provide the skills necessary to independently select relevant

Towards Applying Agile Practices To Bioinformatics Software Development
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ABSTRACT The bioinformatics software developments industry represents one of the fastest growing fields. As a result of the lack of software engineering practices in the developments and the complex nature of bioinformatics software developments, there is a strong need

An Efficient Searching Algorithm for Data Mining in Bioinformatics
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ABSTRACT Bioinformatics is the application of computational techniques to analyze the Information associated with bimolecular on a large-scale. Bioinformatics is the science of storing, extracting, organizing, analyzing, interpreting and utilizing Information from

Applied Biomechanics and Bioinformatics for Analysis of Limb Lengthening Research
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Abstract:Biomechanics demonstrated by the variety of topics associated with physical therapy such as exercise, sports, neuromuscular control, energetics, and locomotor apparatus. Biomechanical treatment related to physical and mechanical components of

Journal of Bioinformatics and Proteomics Review
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Abstract Carnosol and resveretrol are two natural compounds with potent antioxidant activity. These two are at various stages of research independently on various types of cancer. Till the time many of researchers used carnosol and resveretrol for cancer

Representation learning of sequential data with application in bioinformatics
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Abstract:This paper presents a brief overview of approaches for handling sequential data and representation learning based on the neural networks. Recurrent neural networks are described as an approach for sequence learning. We discuss problems which arise when

Isolation, cloning and bioinformatics analysis of ß-amyrin 11-oxidase coding sequence from licorice
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Abstract Licorice is the roots and stolons of Glycyrrhiza uralensis which have several chemical compounds. Triterpene saponins such as glycyrrhizin and glycyrrhetinic acid and flavonoids like liquiritin, isoliquiritigenin and glabron are main compounds detected in The 12th edition of the International Symposium on Bioinformatics Research and Applications (ISBRA 2016) was held during June 5–8, 2016, in Minsk, Belarus. The symposium provides a forum for the exchange of ideas and results among researchers,

International Journal of Computational Biology and Bioinformatics (IJCOB)
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A bstract It has been estimated that autoimmune diseases are the top leading causes of death among women in all age groups beyond 65 years. It is the third most common ailment in the developing countries after cancer and heart disease. According to WHO (2014)

Bioinformatics in Drug Discovery a Review
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Abstract---The drug discovery process was beginning in 19th century by John Langley in 1905 when he proposed the theory of respective substances. Drug discovery is the step- bystep process by which new candidate drugs are discovered. Bioinformatics deals with

Natalio (2010) Learning pathway-based decision rules to classify microarray cancer samples. In: 25th German Conference on Bioinformatics 2010, 20-22 Sept
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This dissertation selects twenty companies in oil and gas industry randomly. By comparing their increased percentages in share prices in the period between 2002 and 2006, the companies are categorised into two groups: well performed and under performed

International Journal of Computational Biology and Bioinformatics (IJCOB)
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A bstract Staphyloccocus aureus have emerged as a pathogen which commonly causes skin infections, respiratory infections and endocarditis. The structure of LuKF shows how a channel forming toxin masks protein-protein and protein-membrane interfaces prior to cell

BlocksReader: A Bioinformatics Tool to Aid in Information Retrieval and Data Visualization Based on the BLOCKS Database
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Abstract We present a tool known as BlocksReader, developed in Matlab, to aid in Information retrieval and data visualization in Bioinformatics. BlocksReader works by taking as input the entire BLOCKS database and storing the protein sequences as vectors. Using

Arcady R. Mushegian is Director of Bioinformatics Research at the Stowers Institute for Medical Research (Kansas City, Missouri, USA) and Professor of Microbiology
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David Kristensen is a Postdoctoral Fellow at the National Center for Biotechnology Information (NLM, NIH, Bethesda, Maryland, USA). Yuri I. Wolf is an Associate Investigator at the National

APPLICATION OF BIOINFORMATICS IN DRUG DISCOVERY
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ABSTRACT Tools of bioinformatics can supplement and replace the traditional drug discovery process. The traditional process involve extraction, isolation and characterization of a compound or synthesize one in laboratory, followed by a series of pharmacological

Study of congenital heart disease, Parkinson's and haemolytic aneamia with the help of protein structure prediction method HMM using Bioinformatics
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Abstract Protein structure prediction is one of the method by which we can predict the helix, sheets and threads available on protein complex molecule. HMM (homology Molecular Modeling) is one the method classified in 3D structure prediction provides you the

Bioinformatics approach for prediction of functional coding/non-coding simple polymorphisms (SNPs/Indels) in human BRAF gene.
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Abstract BRAF, a member of the RAF family, is a protein kinase that is encoded by the BRAF gene. The RAF family of proteins includes three isoforms: ARAF, BRAF, CRAF and each isoform plays a role in the RASRAF pathway. Mutations in this gene are associated with

Bioinformatics analysis of few Zinc metalloproteases from anoxygenic phototrophic bacteria
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ABSTRACT Metalloproteases from nine photosynthetic bacterial species were analyzed and presented in this communication. The composition of alanine, glycine and leucine, valine was high while low concentrations of asparagines, histidine, tyrosine, tryptophan, cysteine

Phylogeny and Bioinformatics Study on Leaf Tissue Genes for Selected Elite Cultivars of Plantain (Musa paradisiaca L) in the Rain Forest Ecology of Nigeria
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ABSTRACT Aims: To show that phylogenetic and bioinformatics study could be very crucial to the survival and adaptation of elite plantain species that are threatened by rapid changes in environment, urbanization, genetic erosion and climate in the rain forest ecology of

Bioinformatics tools for the analysis of macromolecular structures
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Abstract Computational analysis of biological macromolecules and prediction of their properties are important both for their research and biotechnological applications. This thesis is about the novel algorithms and methods for the analysis of structure and function

01605, USA 3 Department of Mathematics, Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48104, USA*
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Abstract Migrating Eastern North American monarch butterflies use a time-compensated sun compass to adjust their flight to the southwest direction. While the antennal genetic circadian clock and the azimuth of the sun are instrumental for proper function of the compass, it is

A bioinformatics analysis reveals a group of MocR bacterial transcriptional regulators linked to a family of genes coding for membrane proteins
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Abstract The MocR bacterial transcriptional regulators are characterized by an N-terminal domain, 60 residue long on average, possessing the winged-helix-turn-helix architecture (wHTH) responsible for DNA recognition and binding, linked to a large C-terminal domain



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