Here is the list Bioinformatics courses offered around the world

US

• Baylor College of Medicine, USA Ph.D. in structural and computational biology and molecular biophysics
• Boston University, USA M.S. and Ph.D. program in bioinformatics
• Carnegie Mellon, USA B.S., M.S. and Ph.D. Merck Computational Biology and Chemistry Program
• George Mason University, USA M.S. and Ph.D. in bioinformatics and computational biology
• Georgia Institute of Technology, USA M.S. in bioinformatics; Ph.D. in Bioinformatics and Computational Biology
• Indiana University, USA B.S. and M.S. in informatics
• Iowa State University, USA Ph.D. program in bioinformatics and computational biology
• Johns Hopkins University, USA Ph.D. program in computational biophysics
• Keck Graduate Institute, USA M.S. and Ph.D. in Bioinformatics and Computational Biology
• Marquette University/MCW, USA M.S. in bioinformatics
• New Jersey Institute of Technology M.S. and Ph.D. in Computational Biology
• North Carolina State University, USA M.S. and Ph.D. in bioinformatics
• Northern Illinois University, USA M.S. specialization in bioinformatics
• Northeastern University, USA M.S. in bioinformatics
• OHIO State University, USA Graduate Program in Biomedical Informatics
• Rensselaer Polytechnic Institute, USA B.S. in bioinformatics and molecular biology
• Rutgers University, USA Ph.D. in computational molecular biology
• Stanford University, USA M.S. and Ph.D. in biomedical informatics
• University of Medicine & Dentistry of New Jersey, USA M.S. and Ph.D. program in biomedial informatics
• University of Medicine & Dentistry of New Jersey, USA M.S. and Ph.D. Bioinformatics track
• University of Albany, USA Ph.D. program in comparative functional genomics
• University of California, Irvine, USA M.S. and Ph.D Informatics in Biology and Medicine
• University of California, Los Angeles, USA M.S. and Ph.D. program in bioinformatics
• University of California, Santa Cruz, USA B.S., M.S. and Ph.D. in Bioinformatics
• University of California, San Diego, USA Ph.D. Bioinformatics
• University of California, San Francisco, uSA M.S. and Ph.D. program in biological and medical informatics
• University of Cincinnati, USA M.S. and Ph.D. Biomedical Engineering-Bioinformatics track
• University of Illinois, Chicago, USA M.S. & Ph.D. Bioinformatics
• University of Memphis, USA M.S. concentration in bioinformatics
• University of Michigan, Ann Arbor, USA M.S. & Ph.D. Bioinformatics
• University of Minnesota, USA M.S. & Ph.D. Bioinformatics
• University of Nebraska, Omaha, USA M.S. and Ph.D. in Bioinformatics
• University of North Carolina, USA M.S. & Ph.D. Bioinformatics and Computational Biology
• University of Pennsylvania, USA B.S., M.S. and Ph.D. programs in Computational Biology/Bioinformatics
• University of Pittsburgh, USA M.S. and Ph.D. in bioimedical informatics
• University of the Sciences in Philadelphia, USA B.S. in bioinformatics
• University of the Sciences in Philadelphia, USA M.S. in bioinformatics
• University of Southern California, USA M.S. & Ph.D. in Molecular and Computational Biology
• University of Texas at Austin, USA Ph.D. in Cell and Molecular Biology-Structural Biology and Bioinformatics track
• University of Texas at El Paso, USA M.S. in bioinformatics
• University of Washington, Seattle, USA Ph.D. Graduate program in computational molecular biology
• University of Wisconsin-Madison, USA Graduate Certificate in Bioinformatics
• University of Wisconsin-Parkside, USA B.S. Molecular Biology & Bioinformatics; M.S. Applied Molecular Biology
• Virgina Tech, USA Graduate program in bioinformatics
• Washington University St Louis, USA Graduate program in computational biology
  

Canada

• Bioinformatics Training Program for Health Research (M.Sc. or Ph.D. in Bioinformatics)
• Seneca College, Toronto (post-graduate diploma in Bioinformatics)
• University of Toronto (Program in Proteomics and BioInformatics)
• Simon Fraser University
• University of British Columbia
• University of Victoria
• University of Alberta
• The University of Calgary, Faculty of Medicine, The O'Brien Centre offers Bachelor of Health Sciences program (BHSc) in Bioinformatics
• University of Lethbridge
• University of Saskatchewan
• University of Manitoba
• Brock University
• Carleton University
• McMaster University
• Queen's University
• University of Guelph
• University of Ottawa
• University of Toronto
• University of Waterloo offers Undergraduate research in Bioinformatics
• University of Western Ontario
• Wilfrid Laurier University
• York University
• Concordia University
• McGill University
• Université de Montréal
• Mount Allison University
• University of New Brunswick
• Dalhousie University
• University of Prince Edward Island
• Memorial University of Newfoundland

Europe

UK

• Birkbeck College, University of London (Accredited online course in protein structure) M.Sc. in molecular modelling and bioinformatics
• Cranfield Centre for Bioinformatics and IT - MSc. Bioinformatics
• Oxford University - Part-time MSc. in Bioinformatics
• University of Abertay Dundee, UK Information Technology (Bioinformatics) - PGDip/MSc
• University of Exeter - MSc, Diploma and Certificate in Bioinformatics MSc/MRes/PgDip/PgCert in Bioinformatics
• University of Leeds, M.Res. in Bioinformatics
• University of Liverpool, M. Sc. in Biosystems and Informatics
• University of Manchester, Masters Program M.Sc. in bioinformatics, distance learning
• University of Nottingham, Master of Philosophy in Molecular Biology with Bioinformatics
• University of Wales College of Medicine, Cardiff, UK - Masters/Diploma/Postgraduate Certificate in Genetic Epidemiology and Bioinformatics
• University of Glasgow, MRes in Bioinformatics
• University of York, MRes in Bioinformatics
• De Montfort University , MSc programme in Bioinformatics

Sweden

• Uppsala University, Sweden (Basic courses)
• University of Skovde, Sweden (MSc in bioinformatics)
• Chalmers University Masters Program in Bioinformatics

Norway

• University of Bergen, Norway (Masters-level courses)

Germany

• Max Planck Institute for Molecular Genetics and Free University Berlin , PhD programs at the IMPRS-CBSC
• Univ.of Bielefeld, Naturwissenschaftliche Informatik (Master's level course)
• University of Tuebingen, Bioinformatics

Finland

• Helsinki University, Graduate School in Computational Biology, Bioinformatics, and Biometry

France

• Pasteur Institute (France) The bioinformatics courses at the Pasteur Institute are organized with the collaboration of the two largest Parisian scientific universities, Paris VI "Pierre et Marie Curie" and Paris VII "Denis Diderot". The diplomas delivered to students of these courses are considered equivalent to university degrees, for 1998 tuition of about 3 000 French Francs, or $500 US.
  
• Université Montpellier II (IMGT Education - Immunoinformatics) (France)
• Master's/PhD bioinformatique at Universite de Rennes
• Master's/PhD Analyse de Génomes et Modélisation Moléculaire Université Paris
• Master's/PhD "Application des Mathématiques et de l'Informatique à la Biologie" at Université d'Evry
• Master's Bioinformatique at Université Paul Sabatier Toulouse
• Master's/PhD bioinformatique de Bioinformatique et Genomique at Université Versailles St Quentin
• Master's Pro Bioinformatique, Universite de Clermont-Ferrand
• Master's Bioinformatique at Universite de Lille
• Mastere Sciences, Mention: Bioinformatique, Biochimie Structurale et Génomique (BBSG) at Aix-Marseille University

Denmark

• Technical University of Denmark, Center for Biological Sequence Analysis (Master's and Phd courses)
• University of Copenhagen, Bioinformatics Centre offers Master's Programme in Bioinformatics
• Syddansk Universitet offers offers both BSc and MSc level in Bioinformatics

Belgium

• Inter-University DEA/DES (Masters program in Bioinformatics)
• Katholieke Universitiet (Masters program in Bioinformatics)

Switzerland

• Swiss Institute of Bioinformatics (Masters program)

Austria

• Bioinformatics at the Institute of Biomedical Engineering, Graz University of Technology
  

Israel

• Weizmann Institute (Online course materials)

New Zealand

• University of Auckland, New Zealand (BSc (Hons) in bioinformatics)

Australia

• La Trobe University (Basic course)
• University of Melbourne (Bioinformatics stream within BSc degree)
• University of Otago - Dunedin, New Zealand (Basic courses)
• University of Queensland (3rd-year course)
• University of Sydney (BSc program)
• University of New South Wales (Bachelor of Engineering in Bioinformatics Programme)
• Flinders University (Bachelor's Programme in Bioinformatics)

Asia & South Pacific

• BioInformatics Institute, Singapore (Masters program)
• National University of Singapore (Training and workshops)
• Nanyang Technological University, Singapore (Master of Science in Bioinformatics)
• National Tsing Hua University, Taiwan (Undergraduate course)
• University of Hong Kong (Bachelor of Science in Bioinformatics)
• University of Malaya, Malaysia (offers BSc & Msc in Bioinformatics)
• Kebangsaan University, Malaysia (offers Bachelors of Science (Honours) in Bioinformatics)
• Mohammad Ali Jinnah University, Pakistan (offers Bachelor of Science in Bioinformatics)
• COMSATS Institute of Technology, Pakistan (offers Bachelor of Science in Bioinformatics)
• GC University Faisalabad, Pakistan (offers Bachelor of Science in Bioinformatics)- Thanks Rabeea Rasheed

Africa

• Rhodes University, South Africa offers an MSc. in Bioinformatics and Computational Molecular Biology
• South African National Bioinformatics Institute (SANBI), offers an MSc. in Bioinformatics

Advanced Courses and Papers

• BioInformatics Institute, Singapore (Ph.D Program)
• Bibliography on Computational Gene Recognition (Rockefeller University)
• Evaluating Regularizers for Estimating Distributions of Amino Acids (Paper by Kevin Karplus, UC Santa Cruz)
• Iowa State University, PhD Program in Bioinformatics and Computatinal Biology (Ames, Iowa)
• Perl Programing Course for Bioinformatics and Internet (Weizmann Institute of Science, Israel)
• Rutgers University, PhD Program in Computational Biology (Newark, New Jersey)
• Sequence Alignment and Modeling System (Documentation for SAM)
• Technical University of Denmark, PhD Course in Biological Sequence Analysis and Protein Modeling
• Training Program for Bioinformaticians in Health Research - Vancouver (M.Sc. and Ph.D. Programs)
• University of Pennsylvania (Doctoral Program and Postdoctoral Program )
• USC (PhD Program)
• Virtual School of Natural Sciences (Online Courses)
• De Montfort University, U.K, BioHealth Informatics research team offers MPhil and PhD studies in various computational biology and health related subjects

Here is the list Bioinformatics courses offered around the world