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18.11.2013: Bioinformatics Seminars 2013-2014 (Information)

2013-2014 Seminars Announcement

Announcement file:

FILE

26.02.2013: Workshop on Computational Intelligence Applications in Bioinformatics (CIAB2013) (Conference)

The aim of CIAB2013 workshop is to serve as an interdisciplinary forum for bringing together specialists and to deal with problems from the field of Biology, Bioinformatics, Computational Biology, Chemical Informatics, and Bioengineering. Issues related to the theory of Computational Intelligence techniques, as well as applications in Bioinformatics and Computational Biology will be addressed in this workshop in order to motivate research in new trend-setting directions. This is the third year of the existence of the CIAB2013 workshop. CIAB2011 took place in Corfu, Greece, 15-18 September, 2011 at the 12th EANN/7th AIAI Joint Conference (http://delab.csd.auth.gr/eann2011/) and CIAB2012 in London, United Kingdom, 20-23 September, 2012 at the 13th EANN Conference.

 

Announcement file:

FILE

08.11.2012: Tactical Meetings (Information)

The weekly meeting of our group are going to take place each Monday 13:00-15:00 in Π200 class.

27.09.2012: 1st Workshop on Algorithms for Data and Text Mining in Bioinformatics (WADTMB 2012) (Information)

Important Dates:
Paper submission: April 29, 2012
Notification of acceptance/rejection: May 26, 2012
Camera-ready submission: June 4, 2012
Early registration: June 04, 2012
Workshop dates: To be announced

Program Chairs
Athanasios Tsakalidis
University of Patras, Greece

Christos Makris
University of Patras, Greece

Organising Chairs
Marina Ioannou
University of Patras, Greece
ioannouz@ceid.upatras.gr

Yannis Plegas
University of Patras, Greece

Evangelos Theodoridis
University of Patras, Greece

Workshop Program Committee (not complete)

  • Athanasios Tsakalidis, University of Patras, Greece
  • Christos Makris, University of Patras, Greece
  • Vasilis Megalooikonomou, University of Patras, Greece
  • Evangelos Theodoridis, University of Patras, Greece

Workshop Aim: The aim of this workshop is to bring together researchers that are interested in designing, developing and applying efficient data and text mining techniques for discovering the underlying knowledge existing in biomedical data.

Bioinformatics is an emerging field of science that plays a crucial role in managing, processing and computationally analyzing biological and biomedical data such as sequences, gene expressions and pathways. Biomedical researchers face the fundamental issue of making efficient use of a tremendous amount of data that is produced and deposited in public, in order to improve and enhance their understanding of complex biomedical systems. As a result, there is an urgent need for novel efficient computational methods and tools to facilitate the process of managing and discovering useful patterns and knowledge from these large biomedical data repositories.

Data mining plays an essential role in Bioinformatics since it is the process of automatic discovering of hidden meaningful and useful patterns and correlations in large amounts of data. Data mining approaches provide tools for dealing with biomedical problems such as protein structure prediction, efficient clustering of gene expression data and efficient gene classification. Also, of significant importance is biomedical text mining, that is the process of automatically exploiting enormous amount of knowledge available in biomedical literature such as automatic extraction of protein-protein interactions, named entity recognition, text classification and terminology extraction.

Although considerable progress has been made recently in these areas, many of the fundamental issues in bioinformatics such as the ability of completely automatic extraction of useful information from structured or unstructured data remain open challenging tasks.
The proposed workshop aims at giving the opportunity to researchers to present their original work on issues pertaining to data and text mining in bioinformatics. We encourage papers that present novel mining techniques and tools for the following tasks:

  • Biomedical Database management
  • Gene expression analysis
  • Protein structure prediction
  • Prediction of protein-protein interaction
  • Text Mining in Biomedical Literature
  • Web Mining Bioinformatics applications

Submission:
All papers should be submitted by email to both Program Chair Christos Makris makri@ceid.upatras.gr and cc'ed to Organising Chair Marina Ioannou ioannouz@ceid.upatras.gr. Papers should be submitted either in a doc or in a pdf form and they should be peer reviewed by at least 2 academic referees. Papers should not exceed 10 pages formatted according to the LNCS Springer style.

Publication:
Accepted papers will be presented orally in the conference for 20 minutes and they will be published in the Proceedings of the main event. They will be also considered for potential selection for publication in the Special Issues that will be edited.

 

20.09.2012: Workshop on Computational Intelligence Applications in Bioinformatics (CIAB2012) (Information)

Bioinformatics is the field of science in which Biology, Computer Science, and information technology merge to form a single discipline. The ultimate goal of the field is to enable the discovery of new biological insights as well as to create a global perspective from which unifying principles in Biology can be discerned. The analysis and interpretation of biological data is an extremely hard task due to their complexity, size and noisy nature. Recent applications of Computational Intelligence (CI) in this area suggest that they are well-suited to this area of research. This workshop will highlight applications of CI to a broad range of topics. Particular interest will be directed towards novel applications of CI approaches to problems in these areas.
Computational Intelligence, a sub-branch of Artificial Intelligence, studies, mostly nature inspired, adaptive mechanisms to facilitate intelligent behavior in complex and changing environments. Some of the most important CI representative methods are: Artificial Neural Networks, Evolutionary Algorithms, Swarm Intelligence, Artificial Immune Systems, Ant-colony Optimization, and Fuzzy Systems. Individual techniques from these CI paradigms, as well as hybridizations between CI approaches, have been applied successfully to solve Applied Biology, Bioinformatics and Molecular Biology problems.
The aim of CIAB2012 workshop is to serve as an interdisciplinary forum for bringing together specialists and to deal with problems from the field of Biology, Bioinformatics, Computational Biology, Chemical Informatics, and Bioengineering. Issues related to the theory of Computational Intelligence techniques, as well as applications in Bioinformatics and Computational Biology will be addressed in this workshop in order to motivate research in new trend-setting directions. This is the second year of the existence of the CIAB2012 workshop. CIAB2011 took place in Corfu, Greece, 15-18 September, 2011 at the 12th EANN/7th AIAI Joint Conference (http://delab.csd.auth.gr/eann2011/).
CIAB2012 welcomes paper submissions introducing and implementing Computational Intelligent techniques to address various problems in Bioinformatics and Computational Biology. Our aim is to bring together researchers, engineers, developers and practitioners from academia to industry working in multi-disciplinary area and technically converging areas. Topics of interest include, but are not limited to:

  • Systems Biology
  • Molecular Sequence Alignment and Analysis
  • RNA and protein folding and structure prediction
  • Gene expression analysis from microarrays
  • Protein-Protein interactions
  • Biological Networks
  • Biological Processes
  • Biological and Medical Ontologies
  • Computational Proteomics and Genomics
  • In-silico Optimization of Biological Systems
  • High-Throughput Data Analysis (microarrays, mass spectrometry, EST, NGS etc.)
  • Analysis of Large Biological Data Sets
  • Medical Image Analysis and Pattern Recognition

Authors are invited to submit original and significant research contributions in the aforementioned areas. All submissions will be reviewed by at least two reviewers. Manuscripts should be prepared according to the standard format of regular papers specified in EANN conferences and should be restricted to a maximum of 10 pages. Detailed instructions for preparing and submitting the manuscript are provided at http://www.eann.org.uk/eann2012/sbmissions.php. Workshop papers will be published in the EANN 2012 proceedings in Springer CCIS Series. Furthermore, it will be investigated the possibility of publishing extended versions of the presented research papers in an edited book, issued by some international publisher or in a special issue of an international research journal.
For every question about the manuscripts preparation, their submission and the organization of the workshop authors could contact us in: sfg@teikal.gr, mavroudi@ceid.upatras.gr or theofilk@ceid.upatras.gr.

Important Dates

Paper submission deadline : May 15, 2012

Notification of acceptance : May 30, 2012

Camera-ready copy : June 15, 2012

Program Committee

Prof. Spiridon D. Likothanassis
Professor,
Department of Computer Engineering and Informatics,
University of Patras
26500 Patras, Greece
e-mail: likothan@ceid.upatras.gr

Dr. Efstratios F. Georgopoulos,
Associate Professor,
Technological Educational Institute (T.E.I.) of Kalamata
Antikalamos, 24100, Kalamata, Greece
e-mail: sfg@teikal.gr

Dr. Seferina Mavroudi
Assistant Professor (P.D. 407/80), Department of Computer Engineering and Informatics, University of Patras
26500 Patras, Greece  e-mail: mavroudi@ceid.upatras.gr

Dr Adam Adamopoulos
Assistant Professor, Department of Medicine,
University of Thrace, 681 00 Alexandroupoli, Greece e-mail: adam@med.duth.gr

Prof. Athanasios Tsakalidis
Professor,
Department of Computer Engineering and Informatics,
University of Patras
26500 Patras, Greece
e-mail: tsak@cti.gr

Dr. Sofia Kossida
Investigator
Bioinformatics & Medical Informatics Team
Foundation for Biomedical Research,
Academy of Athens
28 Panepistimiou Street, Athens, 10679, Greece
e-mail: skossida@bioacademy.gr

Dr. Horacio Pérez-Sánchez
Computer Engineering Department
School of Computer Science
University of Murcia, Spain
e-mail: horacio@um.es

Prof. Alex Gammerman
Professor of Computer Science
Royal Holloway, University of London
Egham Hill, EGHAM, TW20 0EX, United Kingdom
e-mail: alexanderyg@gmail.com

Dr. Vassilis P. Plagianakos
Assistant Professor Department of Computer Science and Biomedical Informatics
University of Central Greece
2-4 Papassiopoulou Street, Lamia, 35100, Greece
e-mail: vpp@ucg.gr

Dr. George D. Magoulas
Professor of Computer Science London Knowledge Lab- www.lkl.ac.uk
Department of Computer Science and Information Systems
Birkbeck College, University of London
e-mail: gmagoulas@dcs.bbk.ac.uk

Dr. Panos Kalnis
Associate Professor
Division of Mathematical and Computer Sciences and Engineering
King Abdullah University of Science and Technology (Kaust)
Thuwal 23955, Saudi Arabia
e-mail: panos.kalnis@kaust.edu.sa

Dr. Charalampos Moschopoulos
Faculty of Engineering - ESAT/SCD,
Katholieke Universiteit Leuven,
Kasteelpark Arenberg 10, 3001, Leuven-Heverlee, Belgium
e-mail: cmoschop@esat.kuleuven.be

Dr. Ioannis Valavanis
Post-doctoral Researcher
Institute of Biological Research and Biotechnology, National Hellenic Research Foundation (NHRF)
48 Vassileos Constantinou Ave., 11635 Athens, Greece
e-mail: ivalavan@eie.gr

11.09.2012: First meeting for 2012-2013 (Meeting)

The first meeting of the Bioinformatics Group of the Department of Computer Engineering and Informatics was conducted today 12:00-14:00 in class Π200. The next meeting of the group is arranged for Monday 17th September, 12:00-14:00 in Π200.