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Bioinformatics, a hybrid science that links biological data with techniques for information storage, distribution, and analysis to support multiple areas of scientific research, including biomedicine. Bioinformatics is fed by high-throughput data-generating experiments, including genomic sequence. Bioinformatics and computational biology involve the use of techniques including applied mathematics, informatics, statistics, computer science, artificial intelligence, chemistry and biochemistry to solve biological problems usually on the molecular level. Research in computational biology often overlaps with systems

What is bioinformatics A proposed definition and overview of the field
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Summary Background: The recent flood of data from genome sequences and functional genomics has given rise to new field, bioinformatics which combines elements of biology and computer science. Objectives: Here we propose a definition for this new field and review

Serendipity in bioinformatics the tribulations of a Swiss bioinformatician through exciting times!
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This is a personal recollection of the events that led me to develop software tools and databases in the context of what has recently been termed proteomatics ( bioinformatics in the context of proteomics). As will be manifest from this article, the creations of PC/Gene,

Bioinformatics for next generation sequencing
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The transforming aspect of the Human Genome Project was not the completion of the genome sequence itself, but rather the technologies that enabled, and were enabled by, the sequencing of that first reference genome. The evolution of omic science through microarray

TAMBIS: Transparent access to multiple bioinformatics information sources.
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Abstract The TAMBIS project aims to provide transparent access to disparate biological databases and analysis tools, enabling users to utilize a wide range of resources with the minimum of effort. A prototype system has been developed that includes a knowledge base

RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database
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RADARS, a rapid, automated, data archiving and retrieval software system for highthroughput proteomic mass spectral data processing and storage, is described. The majority of mass spectrometer data files are compatible with RADARS, for consistent

Training for bioinformatics and computational biology
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The explosive increase in biological information produced by large-scale genome sequencing and gene/protein expression projects has created a demand that greatly exceeds supply for researchers trained both in biology and in computer science two quite

Fuzzy logic in medicine and bioinformatics
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The purpose of this paper is to present a general view of the current applications of fuzzy logic in medicine and bioinformatics . We particularly review the medical literature using fuzzy logic. We then recall the geometrical interpretation of fuzzy sets as points in a fuzzy John Overington holds a first degree in chemistry, and studied for his PhD on comparative protein modeling, drug design, and sequence-structure relationships with Sir Tom Blundell FRS, at Birkbeck College, London. After a postdoctoral fellowship with the Imperial Cancer

The early days of bioinformatics publishing
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Abstract A brief history of the early days of publishing in the bioinformatics field is presented. When two fields of science discover common ground, it can provide great exhilaration for the individuals exploring the new territory. For their colleagues,

How will bioinformatics influence metabolic engineering
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Abstract: Ten microbial genomes have been fully sequenced to date, and the sequencing of many more genomes is expected to be completed before the end of the century. The assignment of function to open reading frames (ORFs) is progressing, and for some

NIH working definition of bioinformatics and computational biology
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Bioinformatics and computational biology are rooted in life sciences as well as computer and information sciences and technologies. Both of these interdisciplinary approaches draw from specific disciplines such as mathematics, physics, computer science and engineering,

Experiences with e-Science workflow specification and enactment in bioinformatics
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Abstract Workflow techniques form an important part of in-silico experimentation within the bioinformatics domain and potentially allow the eScientist to describe and enact their experimental processes in a structured, repeatable and verifiable way. Bioinformaticians

Network protocol analysis using bioinformatics algorithms
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ABSTRACT Network protocol analysis is currently performed by hand using only intuition and a protocol analyzer tool such as tcpdump or Ethereal . This paper presents Protocol Informatics, a method for automating network protocol reverse engineering by

Bioinformatics and discovery: induction beckons again
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The problem of induction``Logical deduction is a process by which the truth of a general statement entails the truth of a particular statement. For example, if it is true that``all men are mortal, then we can deduce from the statement Socrates is a manthat Socrates is mortal.

A practitioners guide to data management and data integration in bioinformatics
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Integration of a large and widely diverse set of data sources and analytical methods is needed to carry out bioinformatics investigations such as identifying and characterizing regions of functional interest in genomic sequence, inferring biological networks, and The recent accumulation of information from genomes, including their sequences, has resulted not only in new attempts to answer old questions and solve longstanding issues in biology, but also in the formulation of novel hypotheses that arise precisely from this wealth Biological systems are inherently stochastic and uncertain. Thus, research in bioinformatics where computer technologies are applied to the management of biological data, and in computational biology, where computational models are built for modeling and analysis of

Artificial intelligence techniques for bioinformatics
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Abstract This review article aims to provide an overview of the ways in which techniques from artificial intelligence can be usefully employed in bioinformatics both for modelling biological data and for making new discoveries. The paper covers three techniques: The discovery of the double-helix structure of DNA by Watson and Crick more than fifty years ago was the starting point of a new era in molecular biology. Since then, our knowledge of biological structures and processes has grown tremendously. But many of these advances

Proteus, a grid based problem solving environment for bioinformatics : Architecture and experiments
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Abstract Bioinformatics can be considered as a bridge be-tween life science and computer science. Biology requires high and large computing power to performance biological applications and to access huge number of distributed and (often) heterogeneous

Bioinformatics
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Aim and Scope INTERNATIONAL JOURNAL OF ADVANCED BIOTECHNOLOGY BIOINFORMATICS is an online, freely available, peer reviewed journal that endeavors to rapidly publish original, authentic and fundamental RESEARCH PAPERs, review articles, case

Statistical learning and kernel methods in bioinformatics
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In this Section, we formalize the problem of pattern recognition as that of classifying objects called pattern into one of two classes. We introduce a simple pattern recognition algorithm that illustrates the mechanism of kernel methods. Suppose we are given empirical data ¤¦¥§ § ¤¦¥!

Ontology-based integration for bioinformatics
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Abstract Information integration systems support researchers in bioinformatics to retrieve data from multiple biological data sources. In this paper we argue that the current approaches should be enhanced by ontological knowledge. We identify the different types of

Computational biology bioinformatics : a gentle overview
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2. What is Bioinformatics /Computational Biology Computational Biology/ Bioinformatics is the application of computer sciences and allied technologies to answer the questions of Biologists, about the mysteries of life. A mere application of computers to solve any problem

Applying task analysis to describe and facilitate bioinformatics tasks.
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Abstract Objective: To document bioinformatics tasks currently performed by researchers in genomics and proteomics in an effort to recognize unmet informatics needs and challenges, identify system features that would enhance the performance of those tasks, and inform the

Comparative proteome bioinformatics : identification of a whole complement of putative protein tyrosine kinases in the model flowering plant Arabidopsis
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Phosphorylation by protein tyrosine kinases is crucial to the control of growth and development of multicellular eukaryotes, including humans, and it also seems to play an important role in multicellular prokaryotes. A plant tyrosine-specific kinase has not been

3.16 Bioinformatics Algorithms: Sequence Analysis, Genome Rearrangements, and Phylogenetic Reconstruction
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We introduce and study the problem of compressed indexed sequence of strings, ie representing indexed sequences of strings in nearly-optimal compressed space, while preserving provably good performance for the supported operations. We present a new data

A bioinformatics approach for the phenotype prediction of non-synonymous single nucleotide polymorphisms in human cytochrome P450s
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Page 1. DMD #26047 1 TITLE PAGE: A BIOINFORMATICS APPROACH FOR THE PHENOTYPE PREDICTION OF NON- SYNONYMOUS SINGLE NUCLEOTIDE POLYMORPHISMS IN HUMAN CYTOCHROME P450S LIN-LIN WANG, YONG LI, SHU-FENG ZHOU Department of Nutrition

Bioinformatics based strategies for rapid microorganism identification by mass spectrometry
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Plamen A. Demirev, Andrew B. Feldman, and Jeffrey S. Lin e review approaches for microorganism identification that exploit the wealth of information in constantly expanding proteome databases. Masses of an organisms protein biomarkers are experimentally

Identification of probable genomic packaging signal sequence from SARS-CoV genome by bioinformatics analysis
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2Shanghai Center for Bioinformation Technology, Shanghai 201203; 3Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences,

Bringing sequences to life: How bioinformatics corporealizes sequence data
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Sequence databases have become visible through the heavy publicity associated with the Human Genome Project. This paper looks at some of the emerging artefacts and systems developed to read, write, order and visualise sequence data and other kinds of biological

Challenges in bioinformatics for statistical data miners
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Abstract Starting with possible definitions of statistical data mining and bioinformatics this article will give a general side-by-side view of both fields, emphasising on the statistical data mining part and its techniques, illustrate possible synergies and discuss how statistical data

Parallelizing bioinformatics applications with MapReduce
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Abstract Current bioinformatics applications require both management of huge amounts of data and heavy computation: fulfilling these requirements calls for simple ways to implement parallel computing. MapReduce is a general-purpose parallelization technology that

Application of support vector machines in bioinformatics
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ABSTRACT Recently a new learning method called support vector machines (SVM) has shown comparable or better results than neural networks on some applications. In this thesis we exploit the possibility of using SVM for three important issues of bioinformatics : the

Optimizing the performance of probabilistic neural networks in a bioinformatics task
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ABSTRACT: A self adaptive probabilistic neural network model is proposed. The model incorporates the Particle Swarm Optimization algorithm to optimize the spread parameter of the probabilistic neural network, enhancing thus its performance. The proposed approach is

Intelligent control and biological regulation for bioinformatics
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Abstract Regulation and control in biological processes are the center of life. Living organisms grow and reproduce. They maintain their structures and respond to their environments. All these processes are done through regulation and control. This paper

An overview of multiple sequence alignments and cloud computing in bioinformatics
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Multiple sequence alignment (MSA) of DNA, RNA, and protein sequences is one of the most essential techniques in the fields of molecular biology, computational biology, and bioinformatics . Next-generation sequencing technologies are changing the biology

Basic formal ontology for bioinformatics
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Two senses of ontologycan be distinguished in the current literature. First is the sense favored by information scientists, who view ontologies as software implementations designed to capture in some formal way the consensus conceptualization shared by those

Integration of bioinformatics resources for functional analysis of gene expression and proteomic data
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1. Abstract 2. Introduction 3. Data integration and analysis 3.1. Data Sources 3.2. Data mapping 3.3. Data integration 3.4. Data search and retrieval 3.4. 1. Entry retrieval and batch retrieval 3.4. 2. Peptide search 3.4. 3. Text search 3.4. 4. Sequence similarity 3.5. Data

Support vector machines in bioinformatics
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The initial goal of the Human Genome Project to produce a draft sequence of the human genome has been achieved in summer 2000 and an advanced assembly is reported in february 2001. But knowledge of the genomic sequence is just the first step towards an

Bioinformatics : use in bacterial vaccine discovery
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ABSTRACT Bioinformatics has now become a common laboratory name for groups studying genomic sequences. It is composed of many different, yet interrelated scientific fields such as genomics, proteomics, and transcriptional profiling. The availability of complete genomic

Online database and bioinformatics toolbox to support data mining in cancer cytogenetics
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Figure 1. Cytogenetic data transformation, using comparative genomic hybridization (CGH) data as example.(A) The various International System for Cytogenetic Nomenclature (ISCN)- related annotation formats found in the literature are transformed to standard reverse in situ

Soft computing methodologies in bioinformatics
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Abstract Bioinformatics is a promising and innovative research field in 21st century. Despite of a high number of techniques specifically dedicated to bioinformatics problems as well as many successful applications, we are in the beginning of a process to massively integrate

Data integration in bioinformatics : current efforts and challenges
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With the rapid advancements in next-generation sequencing (NGS) technologies and the consequently fast-growing volume of biological data, a diversity of data sources (databases and web servers) have been created to facilitate data management, accessibility, and With the success of an expanding array of genome sequencing projects, the number of known protein sequences has been increasing exponentially. However, the sequences on their own cannot tell what each protein does in cell. Although protein structure information is

Hierarchical text categorization and its application to bioinformatics
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Abstract In a hierarchical categorization problem, categories are partially ordered to form a hierarchy. In this dissertation, we explore two main aspects of hierarchical categorization: learning algorithms and performance evaluation. We introduce the notion of consistent

Emergent unsupervised clustering paradigms with potential application to bioinformatics
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1. Abstract 2. Introduction 3. Unsupervised clustering with integrated feature and order selection 3.1. Introduction 3.2. Review of recent methods 4. Semisupervised clustering 4.1. Introduction 4.2. Review of recent methods 4.3. Formulation 4.4. Illustrative Experiment 5. Clustering in the

Comparative analysis of data mining tools and classification techniques using weka in medical bioinformatics
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Abstract The availability of huge amounts of data resulted in great need of data mining technique in order to generate useful knowledge. In the present study we provide detailed information about data mining techniques with more focus on classification techniques as

A comparison of three bioinformatics pipelines for the analysis of preterm gut microbiota using 16S rRNA gene sequencing data
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Copyright: 2015 Plummer E, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are

Grid based virtual bioinformatics laboratory
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Abstract Biotechnologies such as genomics, gene sequencing and highthroughput screening are creating massive volumes and multiple sources of biological and chemical data. However, the volumes of data and the processing power required to analyse it, is

Bacterial bioinformatics : pathogenesis and the genome
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Abstract As the number of completed microbial genome sequences continues to grow, there is a pressing need for the exploitation of this wealth of data through a synergistic interaction between the wellestablished science of bacteriology and the emergent discipline of

Neural networks and machine learning in bioinformaticstheory and applications.
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Abstract. Bioinformatics is a promising and innovative research field. Despite of a high number of techniques specifically dedicated to bioinformatics problems as well as many successful applications, we are in the beginning of a process to massively integrate the

Bioinformatics and reanalysis of subtracted expressed sequence tags from the human ciliary body: identification of novel biological functions
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Purpose: The ciliary body is largely known for its major roles in the regulation of aqueous humor secretion, intraocular pressure, and accommodation of the lens. In this review article we applied bioinformatics to re-examine hundreds of expressed sequence tags (ESTs)

Clinical bioinformatics
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Clinical bioinformatics provides biological and medical information to allow for individualized healthcare. In this review, we describe the uses of clinical bioinformatics . After the analysis of the complete human genome sequences, clinical bioinformatics enables

Bioinformatics and Drug Discovery
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Summary In the past 10 yr, the field of bioinformatics has been characterized by the mapping of many genomes. These efforts have stimulated explosive development of novel bioinformatics and experimental approaches to predict the functions and metabolic role of

On the organization of bioinformatics core services in biology-based research institutes
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With the growth of genomics, research institutes are increasingly confronted with the task of providing computational support to biologists and the provision of computational facilities, both for laboratory-based bioinformaticians and bioinformatics RESEARCH PAPER groups. The optimal

Prediction of epitopes and structural properties of Iranian HPV-16 E6 by bioinformatics methods
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Abstract HPV-16 is the HPV most often linked to cervical carcinoma. E6 of the HPV-16 which expressed early in cancer cells is a target for immune therapeutic methods. In the present study, after fetching the sequence of HPV-16 E6 from NCBI
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