Konstantinos Blekas, Assistant Professor
Department of Computer Science
University of Ioannina

Textbook

Ύλη του μαθήματος

• Sequencing - Poisson Processes (Σημειώσεις)
• Seqeunce Alignment Methods (Κεφ. 6.4) ( Σημειώσεις 1 Σημειώσεις 2 )
• Suffix Trees ( Σημειώσεις 1 Σημειώσεις 2 )
• Random Walks and the BLAST algorithm (Κεφ. 7 και 10)
• Markov Chains Σημειώσεις )
• Hidden Markov Models Σημειώσεις 1 (Rabiner Tutorial) ) Σημειώσεις 2 )
• Sampling Methods: Markov Chain Monte Carlo (MCMC) - Gibbs Sampling (Σημειώσεις για MCMC 1 ) (Σημειώσεις για MCMC 2 )
• Motif Discovery Problem (Σημειώσεις για Gibbs Sampling 1 ) (Παράδειγμα Gibbs Sampling 2 ) (Παράδειγμα Gibbs Sampling 3 )
• Support Vector Machines
• Regression models for sequential data

Ασκήσεις για παράδοση

• Ασκηση 1 (26/3/2012)
• Ασκηση 2 (3/5/2012) Πειραματικά Σύνολα ακολουθιών για μελέτη: Sequences1.mat , Sequences2.mat , tictac.txt
• Ασκηση 3 (11/5/2012)

Υλικό για την Γλώσσα Matlab

• Matlab Tutorial (Greek)
• Matlab Tutorial 1
• Matlab Tutorial 2
• Matlab Tutorial 3

Useful links

• J-Express, a tool for analysing microarray gene expression data
• Clustal W, multiple sequence alignment
• Phylip, phylogenetic analysis.
• Pratt, pattern discovery.
• GCG, Wisconsin Sequence Analysis Package Program Manual.
• PROPHET, UNIX based software package for data analysis.
• RasMol, free program which displays molecular structures.
• MolScript, program for creating molecular graphics in the form of PostScript plot files.
• PairWise and SearchWise, Ewan Birney's excellent tools for sequence alignment and search.
• MEME, Multiple EM for Motif Elicitation

• EMBnet node in Oslo.
• EBI, the EMBL Outstation Hinxton.
• EMBL, Heidelberg.
• EMBnet, the European network for molecular biology.
• BIOSCI, Bionet electronic newsgroups.
• CBS, Center for Biological Sequence Analysis, Technical University of Denmark.
• Expasy, Geneve.
• BIBISERV, Bielefeld University Bioinforrmatics Server.
• Nee-How, The Bioresource Finder
• BSM, Biomolecular Structure and Modelling at UCL.
• Human Genome Project Information
• Sanger centre, Hinxton, England.
• SEQNET, Daresbury, England.
• The Johns Hopkins University BioInformatics Web Server.
• W. M. Keck Center for advanced training in computational biology.
• B3E, Bioinformatics in France.
• UK MRC HGMPRC UK Human Genome Mapping Project Resource Centre.
• NCBI National Center for Biotechnology Information (USA).
• NLM National Library of Medicine (USA).
• CGATBSS, Canadian Genome Analysis & Technology (CGAT) Bioinformatics Support Services.
• DDBJ DNA data bank, Japan.
• GDB Genome Data Base.
• ANGIS Australian National Genomic Information Service.
• ANU Bioinformatics Hypermedia Service.
• HUM-MOLGEN Human Molecular Genetics.
• BioMOO The Virtual Meeting Place for Biologists
• BioBox, Finland.
• Information theory and molecular biology, Tom Schneider's group.
• ISREC (Swiss Institute for Experimental Cancer Research), Bioinformatics Group.
• DoubleTwist
• WWW in Biology, bionet.software.www.
• UCSC Computational Biology.
• Bioinformatics and Computational Biology at George Mason University.
• Computational Biology USC, University of Southern California.
• HUJI, Hebrew University of Jerusalem Hadassah Medical School: The Genomic and BioInformatics Server.
• Centre of Bioinformatics, Peking.
• Bioexchange.com

Meetings:

• Previous meetings
• Lists of meetings:
• Meetings, gopher.
• Meetings for bioscientists, searchable listing.
• WWW Virtual library: conferences.

Introductory papers/courses:

• Books on bioinformatics
• Primer on Molecular Genetics, including glossary.
• Recipe book for molecular sequence analysis (ANGIS).
• Protein Sequence Alignment and Database Scanning, Geoff Barton
• Introduction to sequence comparison, Keith Robison.
• Biocomputing Survival Guide
• EMBnet Biocomputing Tutorials
• Biocomputing Tutorials from EMBnet.
• Virtual School of Natural Sciences at the Globewide Network Academy:
• Biocomputing for everyone, from the VSNS (includes Biocomputing in a nutshell).
• BioComputing WWW course at the VSNS Virtual School of Natural Sciences
• Principles of protein structure WWW course.

University Courses in computational biology:

• Bioinformatics course in Bergen.
• International Master's programmein Bioinformatics at Chalmers University of Technology, Gothenburg, Sweden.
• Computational Molecular Biology at Washington University.
• Keck Center, Pittsburgh, Pennsylvania.
• Medical informatics, Pittsburgh, Pennsylvania.
• The Penn Computational Biology Training Program.
• Medical Information Sciences 214 - Representations and Algorithms for Computational Molecular Biology, Stanford.
• Algorithms for Molecular Biology - Course Homepage , Israel.
• PSB Biocomputing Education workshop
• Computational Biology Course, Hopkins
• Bioinformatics courses at George Mason University.
• Biocomputing Course Resource List
• VSNS Multiple Alignment Resource Page
• How to become a bioinformatics expert, list of European courses.
• University Bioinformatics Programs - list provided by IHCP

Advanced papers/courses/lecture transcripts:

• SAM, Sequence alignment and modeling system (using HMMs).
• Dirichlet mixtures, improving detection of weak homologies.
• Regularizers for estimating amino-acid distributions.
• Bill Pearson on homology search.

Journals on the Web:

• Journal of Computational Biology.
• Bioinformatics, Bioinformatics Online
• CABIOS
• Protein Science.
• Proteins: Structure, Function and Genetics
• Genome Research
• Nature, Genome Gateway
• Nucleic Acids Research
• Journal of Molecular Biology.
• The Bioinformer, published by EBI.
• In Silico Biology, online journal
• PubMed, database of journals.
• Bioinform
• IDEAL, International Digital Electronic Access Library - online abstracts. 

Other related sites:

• International Society for Computational Biology
• The Molecular Biologist's Desk Reference.
• The Bioethics Internet Project,
• ELSI, Ethical, legal and social implications of biotechnology.
• The DNA files, WWW pages of US radio program series on Human Genome research and its applications.
• CBPE, Center for Biotechnology Policy and Ethics.
• Eubios Ethics Institute
• Is a genome like a computer program, Gary Welz.
• DNA Computers, by Yali Friedman.
• PhD thesis on DNA computers

Other collections of links:

• Microarray Informatics Resource Page, a collection of literature and web links.
• Biolinks from Bioplanet
• Biotechnology Software, maintained by The National Biotechnology Information Facility
• BRASS, Bioinformatics Resource for Algorithms, Software and Sequences.
• Showcase for new WWW servers.
• Bio-wURLd.
• List at SEQNET
• The World-Wide Web Virtual Library: Biosciences, Harvard.
• Survey of Molecular Biology Databases and Servers, R. Smith.
• Biologists's Control Panel includes searches of many databases.
• Pedro's BioMolecular Research Tool.
• Amos' WWW links.
• Pasteur Institute.
• Nee-How, The Bioresource Finder
• Web Resources for Protein Scientists, Protein Science.
• Motif Bioinformatics Server, Stanford.
• Search engine biological Web Sites.
• Jeff's biolinks, Yale University.