Bioinformatics

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Bioinformatics is the application of computer science and information technology to the field of biology. (Wikipedia.org)






Conferences related to Bioinformatics

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2019 41st Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC)

The conference program will consist of plenary lectures, symposia, workshops andinvitedsessions of the latest significant findings and developments in all the major fields ofbiomedical engineering.Submitted papers will be peer reviewed. Accepted high quality paperswill be presented in oral and postersessions, will appear in the Conference Proceedings and willbe indexed in PubMed/MEDLINE & IEEE Xplore


2019 IEEE International Conference on Systems, Man and Cybernetics (SMC)

2019 IEEE International Conference on Systems, Man, and Cybernetics (SMC2019) will be held in the south of Europe in Bari, one of the most beautiful and historical cities in Italy. The Bari region’s nickname is “Little California” for its nice weather and Bari's cuisine is one of Italian most traditional , based of local seafood and olive oil. SMC2019 is the flagship conference of the IEEE Systems, Man, and Cybernetics Society. It provides an international forum for researchers and practitioners to report up-to-the-minute innovations and developments, summarize state­of-the-art, and exchange ideas and advances in all aspects of systems science and engineering, human machine systems and cybernetics. Advances have importance in the creation of intelligent environments involving technologies interacting with humans to provide an enriching experience, and thereby improve quality of life.


2019 IEEE International Systems Conference (SysCon)

addresses the discipline of systems engineering,including theory, technology, methodology, andapplications of complex systems, system-of-systems,and integrated systems of national and globalsignificance.

  • 2018 Annual IEEE International Systems Conference (SysCon)

    The Conference addresses the discipline of systemsengineering, including theory, technology, methodology,and applications of complex systems, system-of-systems,and integrated systems of national and globalsignificance. It focuses on Systems Engineering for Complex Systems; and the conference caters to both practitioners andacademics, providing a forum to exchange ideas andexperiences on technology, methodology, applications,study cases, and practical experiences.

  • 2017 Annual IEEE International Systems Conference (SysCon)

    The IEEE International Systems Conference facilitates interactions among communities of interest on system-level problems andapplications. System-level thinking is essential in the worldtoday, not only for technical systems, but also for societyat large. The Conference addresses the discipline of systemsengineering, including theory, technology, methodology,and applications of complex systems, system-of-systems,and integrated systems of national and globalsignificance.

  • 2016 Annual IEEE Systems Conference (SysCon)

    The theme of the IEEE International SystemsConference is Engineering of Complex Systems, to includeSystems-of-systems, Systems Engineering, Systems Integration,and Systems Thinking

  • 2015 Annual IEEE Systems Conference (SysCon)

    The theme of the IEEE International Systems Conference is Engineering of Complex Systems, to include Systems-of-systems, Systems Engineering, Systems Integration, and Systems Thinking.

  • 2014 8th Annual IEEE Systems Conference (SysCon)

    This conference seeks to create an interactive forum forthe advancement of the practice of systems engineeringacross the multiple disciplines and specialty areasassociated with the engineering of complex systems. Theconference will provide a venue for systems engineeringpractitioners, managers, researchers, and educators toexchange innovative concepts, ideas, applications, andlessons learned addressing: Applications-oriented topics on large-scale systemsand system-of-systems in topics noted below

  • 2013 7th Annual IEEE Systems Conference (SysCon)

    Conference addresses systems, complex systems, systems-of-systems, critical systems, and the systems engineering disciplines needed to implement such large-scale or complex systems in the international arena.

  • 2012 6th Annual IEEE Systems Conference (SysCon)

    The IEEE Systems Conference is Engineering Complex Integrated Systems and Systems-of-Systems Implications for Systems Engineering, Systems Integration, and Systems Thinking.

  • 2011 IEEE International Systems Conference (SysCon)

    IEEE International Systems Conference Scope is Engineering of Complex Systems, to include Systems-of-systems, Large-scale Systems Integration, and Systems Engineering and Systems Thinking.

  • 2010 4th Annual IEEE Systems Conference

    The theme of the IEEE Systems Conference is Engineering Complex Integrated Systems and Systems-of-systems Implications for Systems Engineering, Systems Integration, and Systems Thinking.

  • 2009 3rd Annual IEEE Systems Conference

    Engineering Comles Integtared Systems and Systems-of-Systems - Implications for Systems Engineering, Systems Integration, and Systems Thinking

  • 2008 2nd Annual IEEE Systems Conference

    The theme of the IEEE Systems Conference is Engineering Complex Integrated Systems and Systems-of-systems- Implications for Systems Engineering, Systems Integration, and Systems Thinking.

  • 2007 1st Annual IEEE Systems Conference

    The theme of the IEEE Systems Conference is Engineering Complex Integrated Systems and Systems-of-systems - Implications for Systems Engineering, Systems Integration, and Systems Thinking.


GLOBECOM 2019 - 2019 IEEE Global Communications Conference

Provides a full program of technical and professional activities spanning hot topics in voice, data, image and multimedia communications and networking.


2018 24th International Conference on Pattern Recognition (ICPR)

ICPR will be an international forum for discussions on recent advances in the fields of Pattern Recognition, Machine Learning and Computer Vision, and on applications of these technologies in various fields

  • 2016 23rd International Conference on Pattern Recognition (ICPR)

    ICPR'2016 will be an international forum for discussions on recent advances in the fields of Pattern Recognition, Machine Learning and Computer Vision, and on applications of these technologies in various fields.

  • 2014 22nd International Conference on Pattern Recognition (ICPR)

    ICPR 2014 will be an international forum for discussions on recent advances in the fields of Pattern Recognition; Machine Learning and Computer Vision; and on applications of these technologies in various fields.

  • 2012 21st International Conference on Pattern Recognition (ICPR)

    ICPR is the largest international conference which covers pattern recognition, computer vision, signal processing, and machine learning and their applications. This has been organized every two years by main sponsorship of IAPR, and has recently been with the technical sponsorship of IEEE-CS. The related research fields are also covered by many societies of IEEE including IEEE-CS, therefore the technical sponsorship of IEEE-CS will provide huge benefit to a lot of members of IEEE. Archiving into IEEE Xplore will also provide significant benefit to the all members of IEEE.

  • 2010 20th International Conference on Pattern Recognition (ICPR)

    ICPR 2010 will be an international forum for discussions on recent advances in the fields of Computer Vision; Pattern Recognition and Machine Learning; Signal, Speech, Image and Video Processing; Biometrics and Human Computer Interaction; Multimedia and Document Analysis, Processing and Retrieval; Medical Imaging and Visualization.

  • 2008 19th International Conferences on Pattern Recognition (ICPR)

    The ICPR 2008 will be an international forum for discussions on recent advances in the fields of Computer vision, Pattern recognition (theory, methods and algorithms), Image, speech and signal analysis, Multimedia and video analysis, Biometrics, Document analysis, and Bioinformatics and biomedical applications.

  • 2002 16th International Conference on Pattern Recognition


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Periodicals related to Bioinformatics

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Biomedical Engineering, IEEE Reviews in

The IEEE Reviews in Biomedical Engineering will review the state-of-the-art and trends in the emerging field of biomedical engineering. This includes scholarly works, ranging from historic and modern development in biomedical engineering to the life sciences and medicine enabled by technologies covered by the various IEEE societies.


Biomedical Engineering, IEEE Transactions on

Broad coverage of concepts and methods of the physical and engineering sciences applied in biology and medicine, ranging from formalized mathematical theory through experimental science and technological development to practical clinical applications.


Computational Biology and Bioinformatics, IEEE/ACM Transactions on

Specific topics of interest include, but are not limited to, sequence analysis, comparison and alignment methods; motif, gene and signal recognition; molecular evolution; phylogenetics and phylogenomics; determination or prediction of the structure of RNA and Protein in two and three dimensions; DNA twisting and folding; gene expression and gene regulatory networks; deduction of metabolic pathways; micro-array design and analysis; proteomics; ...


Computer

Computer, the flagship publication of the IEEE Computer Society, publishes peer-reviewed technical content that covers all aspects of computer science, computer engineering, technology, and applications. Computer is a resource that practitioners, researchers, and managers can rely on to provide timely information about current research developments, trends, best practices, and changes in the profession.


Computers, IEEE Transactions on

Design and analysis of algorithms, computer systems, and digital networks; methods for specifying, measuring, and modeling the performance of computers and computer systems; design of computer components, such as arithmetic units, data storage devices, and interface devices; design of reliable and testable digital devices and systems; computer networks and distributed computer systems; new computer organizations and architectures; applications of VLSI ...


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Xplore Articles related to Bioinformatics

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Development of technology and engineering: Cases of study of the bioinformatics and biology sistems Master's Degree in Costa Rica

2016 IEEE 36th Central American and Panama Convention (CONCAPAN XXXVI), 2016

This work is based on the Bioinformatics technology developments made on the post graduate course of the Bioinformatics Master's Degree of the University of Costa Rica's Medical School, imparted by Professor Allan Orozco, who is one of the main academic founders of Master's Degree. The biocomputing programs were developed by several students that cover the innovation and development of sequence ...


Bio-Linux as a tool for bioinformatics training

2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE), 2012

Because of the ever-increasing application of next-generation sequencing (NGS) in research, and the expectation of faster experiment turn-around, it is becoming unfeasible and unscalable for analysis to be done exclusively by existing trained bioinformaticians. Instead, researchers and bench biologists are performing at least parts of most analyses. In order for this to be realized, two conditions must be satisfied: (1) ...


Pathway bioinformatics

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003, 2003

Pathway bioinformatics is a subfield of bioinformatics that is concerned with pathway algorithms, ontologies, visualizations, and databases [4]. This talk will provide an overview of the pathway databases and software under development in the bioinformatics research group at SRI International, and will then discuss three pathway algorithms in detail.


Use of open linked data in bioinformatics space: A case study

2013 8th International Symposium on Health Informatics and Bioinformatics, 2013

In the life sciences, semantic web can support many aspects of bio- and health informatics, with exciting applications appearing in areas ranging from plant genetics to drug discovery. Using semantic technologies with open linked data, provides two kinds of advantages: ability to search multiple datasets through a single framework and ability to search relationships and paths of relationships that go ...


Development of dbOGAP: A bioinformatics resource of O-GlcNAcylated proteins and site prediction

2009 IEEE International Conference on Bioinformatics and Biomedicine Workshop, 2009

Protein glycosylation is one of the most common posttranslational modifications (PTMs) with several types. O-GlcNAcylation is an O-linked glycosylation with attachment of beta-N-acetylglucosamine (GlcNAc) to Ser/Thr residues catalyzed by O-GlcNAc transferase (OGA), whose removal is catalyzed by O-GlcNAcase. Unlike mucin-type O-glycosylation, O-GlcNAcylation occurs primarily in nucleocytoplasmic proteins and the monosaccharide is not further extended. Moreover, O-GlcNAcylation is dynamic and often ...


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Educational Resources on Bioinformatics

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IEEE-USA E-Books

  • Development of technology and engineering: Cases of study of the bioinformatics and biology sistems Master's Degree in Costa Rica

    This work is based on the Bioinformatics technology developments made on the post graduate course of the Bioinformatics Master's Degree of the University of Costa Rica's Medical School, imparted by Professor Allan Orozco, who is one of the main academic founders of Master's Degree. The biocomputing programs were developed by several students that cover the innovation and development of sequence alignment programs by using bar codes with color spectrum differentiation. Its includes a web, noise elimination techniques on microarrays, solution algorithms of Smith-Waterman in Delphi language, it's also provides a way to design and implementation of a new system to build workflows (WORFORBIO: Workflows for Bioinformatics) and a text mining system on the Protein Data Bank based on SOLR APACHE and REST. Web services from Medical School's GALAXY server at the NELLY Bioinformatics Cluster were used to make complimentary tests.

  • Bio-Linux as a tool for bioinformatics training

    Because of the ever-increasing application of next-generation sequencing (NGS) in research, and the expectation of faster experiment turn-around, it is becoming unfeasible and unscalable for analysis to be done exclusively by existing trained bioinformaticians. Instead, researchers and bench biologists are performing at least parts of most analyses. In order for this to be realized, two conditions must be satisfied: (1) well designed and accessible tools need to be made available, and (2) researchers and biologists need to be trained to use such tools in order to confidently handle high volumes of NGS data. Bio-Linux is a fully featured, powerful, configurable and easy to maintain bioinformatics workstation and helps on both counts by offering well over one hundred bioinformatics tools packaged into a single distribution, easily accessible and readily usable. Bio-Linux is also accessible in the form of virtual images or on the cloud, thus providing researchers with immediate access to scalable compute infrastructure required to run the analysis. Furthermore this paper discusses how bioinformatics training on Bio-Linux is helping to bridge the data production and analysis gap.

  • Pathway bioinformatics

    Pathway bioinformatics is a subfield of bioinformatics that is concerned with pathway algorithms, ontologies, visualizations, and databases [4]. This talk will provide an overview of the pathway databases and software under development in the bioinformatics research group at SRI International, and will then discuss three pathway algorithms in detail.

  • Use of open linked data in bioinformatics space: A case study

    In the life sciences, semantic web can support many aspects of bio- and health informatics, with exciting applications appearing in areas ranging from plant genetics to drug discovery. Using semantic technologies with open linked data, provides two kinds of advantages: ability to search multiple datasets through a single framework and ability to search relationships and paths of relationships that go across different datasets. The Bio2RDF project creates a network of coherently linked data across the biological databases. As part of the Bio2RDF project, an integrated bioinformatics warehouse on the semantic web is built. In this paper, a use case with a query for multiple distant data sources which are semantically available through Bio2RDF is defined. The validation of the results by traditional search techniques and discussion for future directions is presented.

  • Development of dbOGAP: A bioinformatics resource of O-GlcNAcylated proteins and site prediction

    Protein glycosylation is one of the most common posttranslational modifications (PTMs) with several types. O-GlcNAcylation is an O-linked glycosylation with attachment of beta-N-acetylglucosamine (GlcNAc) to Ser/Thr residues catalyzed by O-GlcNAc transferase (OGA), whose removal is catalyzed by O-GlcNAcase. Unlike mucin-type O-glycosylation, O-GlcNAcylation occurs primarily in nucleocytoplasmic proteins and the monosaccharide is not further extended. Moreover, O-GlcNAcylation is dynamic and often reciprocal to phosphorylation at the same or adjacent Ser/Thr residues. Growing evidences suggest that O-GlcNAcylation is very common and has broad roles in physiology as well as in diseases especially through its interplay with phosphorylation, e.g., regulation of insulin signaling, transcription, and roles in diabetes and neurodegenerative diseases. In contrast to the enormous body of research on cellular roles of phosphorylation, the amount of research on O-GlcNAcylation has been disproportionally small and annotation of O-GlcNAcylated sites in protein databases is currently scarce. An O-GlcNAcylation site prediction program was developed in 2002, but it was based on a small data set with 40 O-GlcNAcylation sites known at that time. Here we seek to develop a database of O-GlcNAcylated proteins and sites, named dbOGAP, and also an O-GlcNAcylated site prediction system based on known sites data in dbOGAP to facilitate annotation and proteomic identification of the O-GlcNAcylation sites. We developed dbOGAP based primarily on O-GlcNAcylated proteins and sites published in peer-reviewed articles dated back to 1984 since it was first described. Most of these proteins were mapped to the UniProtKB protein IDs, except for some that could not be unambiguously mapped. The database currently contains 540 protein entries with experimental O-GlcNAcylation information, and 338 O-GlcNAc sites for 164 proteins. About 59% of these proteins are of humans, and other organisms include rat, mouse, fly and African frog. Among 164 proteins with known O-GlcNAcylation sites, 122 also have both phosphorylation (total 1634) and O-GlcNAc sites (total 263). The gene ontology (GO) profiling showed that the known O-GlcNAcylated proteins have a broad range of functions including developmental process, transcriptional regulation, cell signaling, metabolic regulation, and cellular transport and trafficking. The GO profile also showed that O-GlcNAcylated proteins are primarily nuclear and cytoplasmic, including membrane-associated intracellular proteins. The database is also populated with additional orthologous protein sequences to known O-GlcNAcylated proteins. Additional functional data, including other PTM features, biological pathways and disease information have been integrated to the database. We developed an O-GlcNAcylation site prediction program using support vector machine (SVM). As positive instances, sequence fragments surrounding 322 O-GlcNAcylated Ser/Thr sites were extracted from 157 proteins in dbOGAP, and over 28 thousand sequence fragments surrounding the rest of the Ser/Thr sites in those proteins were assumed as negative instances. Two thirds of this data set was randomly selected as development data and was used for tuning parameters in SVM classifiers, while the rest of the data was set apart as a held-out test data set. To reduce the impact of imbalanced data on the performance of trained classifiers, we explored different ratio of positive to negative instances in a training data set, which was controlled by under-sampling negative instances in a training data set. The optimal parameters of the prediction system were sought in five-fold cross-validation tests conducted on the development data set, and the final classifier trained on the entire development data set was evaluated on the held-out test data set. We used four encoding methods for feature vector extraction, including binary encoding, composition of k-spaced amino acid pairs (CKSAAP), monomer spectrum (MS), and composition of monomer spectrum (CMS). These encoding methods yielded different prediction performance for O-GlcNAcylation sites. The results showed that the method obtained an AUC (area under curve) of ~80% on the test sequence set. The dbOGAP database and the O-GlcNAcylation site prediction program tool are being made Web accessible and the Web resource will be an important bioinformatics tool to facilitate exploration of the broad roles of O-GlcNAcylation in physiology and diseases.

  • Bioinformatics curriculum development and skill sets for bioinformaticians

    The rapid advancement in biological data acquisition technologies has led to massive biological datasets, which requires the development and application of computational methods to analyze and interpret the information. Bioinformatics is the confluence of biology, computer science, and information technology. The Bioinformatics programs are offered by more than 100 universities in the United States, and much more worldwide. Different degree (including BS, MS, and PhD), and certificate programs in Bioinformatics have been performed. The current bioinformatics programs in the US have been studied, regarding their curriculum, program competencies, sizes of the faculty, and student enrollments. The job market is also explored for bioinformatics professional training and career planning. The bioinformatics skill requirements are analyzed. Systematical analysis is carried out by integrating the core competences and curriculum improvements in bioinformatics. The potential employers for bioinformatics professionals are analyzed according to the properties of the companies, such as the sizes, the focus areas, the locations, the skill requirements, and other information. The results provide guidance for bioinformatics curriculum development, such as the minimized courses to cover the basic required skill sets for a bioinformatics student to be a successful bioinformatician. In addition, the analytical results are applied to the redesign of the curriculum in our bioinformatics program which offers MS, PhD, and PhD Minor. In summary, the systematic study of the existing bioinformatics programs in the US and the current market needs for professionals in bioinformatics provide great insight for education in bioinformatics. It helps the curriculum development and reexamination. It also provides the students with the required knowledge for their future career.

  • Bioinformatics approaches in tuberculosis vaccination strategies by whole genome sequence

    Following the availability of whole genome sequence of Mycobacterium tuberculosis (MTB) in public database, the anticipation of its benefits would definitely falls into the contribution towards development of improved vaccine or drug discovery to fight against the fatal disease, tuberculosis (TB). This research aimed to scan the whole genome sequence of MTB by application of bioinformatics approaches to identify most potential candidates for novel or improved TB vaccine since the formal vaccine, BCG has some drawbacks. The whole genome of MTB is scanned to search for potential ORF by performing whole genome BLAST search and data retrieval from SWISSPROT. It is then followed by a series of filtering and screening to fulfil the criteria for selection of rational vaccine targets. Among the filtered results, 196 proteins records had been found and most of them are surface exposed or membrane bound proteins or antigen, which are the important criteria for potential vaccine candidates. This research had yield potential vaccine targets for further vaccination development that will save many efforts of researchers in this field.

  • Bioinformatics tools with deep learning based on GPU

    Due to the rapid increase in biological data dimension and acquisition rate, the traditional analysis methods are unable to achieve acceptable accuracy. Recently, Deep learning technologies have shown outstanding results in many domains; especially in pattern recognition in the field of bioinformatics. In this paper, we provide background of what deep learning and its frameworks. In addition, we review the state-of-the-art algorithms based on GPU to presenting the usage of them to guide computational biologists to know how to leverage deep learning to improve their methods.

  • Comparative study of Middle East respiratory syndrome coronavirus using bioinformatics techniques

    In this study, we collected 141 coding sequences of MERS-CoV from the National Center for Biotechnology and Information (NCBI), including the sequences isolated in Korea in 2015. We conducted the phylogenetic analysis using the Maximum Likelihood method to examine the overall variation patterns among the target sequences, and then, we divided the target sequences into 4 different groups according to occurred countries and host species. Using the codon analyzer named SimFluVar program, we analyzed the codon variation patterns in the wobble position among 4 groups. In order to investigate the effect of codon variations that can change the phenotype of target genes, we compared the transversional substitutions between the Korean-origin sequences and other groups. As a result, we found that the Korea-origin sequences showed very minor differences with those collected from the Saudi Arabia in 2015, whereas other groups which were collected from USA and UK in 2013 and 2014 showed more complicated differences. We also compared the Korea-origin sequences with those of camel-origin sequences, and we found that the substitution pattern was somewhat different with that of human-origin viruses.

  • Evaluating Workflow Management Systems: A Bioinformatics Use Case

    Biological knowledge discovery is a tedious task which relies on computationally intensive analyses to process huge volumes of data and metadata. This task can be facilitated by a well-designed workflow management system, capable of deploying and efficiently orchestrating the scientific analysis. However choosing the right workflow management system remains a critical challenge. In this study, we propose ten metrics for evaluating the efficiency of workflow management systems, and show how the Pegasus-mpi- cluster and Snakemake workflow management systems gave the best overall performance, closely followed by Nextflow.



Standards related to Bioinformatics

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Health Informatics - Personal Health Device Communication - Part 10441: Device Specialization - Cardiovascular Fitness and Activity Monitor

Within the context of the ISO/IEEE 11073 family of standards for device communication, this standard establishes a normative definition of the communication between personal cardiovascular fitness and activity monitoring devices and managers (e.g. cell phones, personal computers, personal health appliances, set top boxes) in a manner that enables plug-and-play interoperability. It leverages appropriate portions of existing standards including ISO/IEEE 11073 ...


Standard for Bioinformatics Data Structures – Framework and Overview

The scope of this project is to develop a framework for standards and protocols, incorporating existing standards where appropriate, to support the bioinformatics sciences with common definition, storage and exchange of information between them. The project will define efforts in the area of nomenclature, databases, access protocols, benchmarks, and validation suites for a variety of bioinformatics data (e.g., genomics, proteomics, ...


Standard for Bioinformatics Standards for Flow Cytometry

This standard supports the common definition, storage and exchange of flow cytometry data. Existing standards are incorporated where appropriate.


Standard for Sequence Ontology

The Sequence Ontology is a well developed current working procedure in the Bioinformatics community, this work will formalize that methodology into a standard. The Sequence Ontology (SO) is designed for three different, but related, purposes. The first of these is to provide a structured controlled vocabulary for the description of features that may be describe by their spatial location upon ...