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Objective:
The course is designed to make the students familier with the basic
molecular biology concepts, computational biology problems and
fundemental computer approaches used for modeling biological processes
and associating them with clinical applications.
Instructor:
Hasan Oğul, Assoc.Prof.Dr., hogul@baskent.edu.tr
Textbook: No main textbook, but the
following are useful:
Fundamental Concepts of Bioinformatics,
D.E.
Krane, M.L.
Raymer, 2003, Benjamin Cummings
Algorithms on strings, trees and sequences,
D. Gusfield, 1997, Cambridge Univ. Press
Computational Molecular Biology, Clote &
Backofen, 2000, Wiley
Journals:
Bioinformatics; Journal of Computational
Biology; BMC Bioinformatics; PLOS Computational Biology; Computational
Biology and Chemistry; Current Bioinformatics; Computers in Biology and Medicine; Computer
Methods and Programs in Biomedicine; Biosystems, FEBS Letters; Journal
of Molecular Biology; Journal of Molecular Modeling; Proteins: Structure, Function and
Bioinformatics.
Assessment:
Class activity (Participation, HWs, Presentations) 1/3
Midterm exam 1/3
Final exam 1/3
Schedule:
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Week 1 |
No class |
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Week 2 |
Cell-DNA-RNA-Protein |
(Slides) |
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Week 3 |
Protein Structure |
(Slides) |
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Week 4 |
Sequence Alignment |
(Slides) |
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Week 5 |
Alignment in Real Life |
(Slides) |
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23 Oct. |
Progressive Multiple Aligment |
Berke |
clustal |
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BLAST |
Berkay |
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Large Sequence Alignment |
Serkan |
mummer |
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Week 6 |
Sequence Classification |
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30 Oct. |
Whole Sequence Classification |
Ahmet |
ESLpred |
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Partial Sequence Classification |
Erhan |
exon |
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Residue Classification |
Gökhan |
secondary |
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Week 7 |
Markov Modeling |
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6 Nov. |
Probabilistic Suffix Tree |
Levent |
pst |
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microRNA Target Prediction |
Deniz |
mirpred |
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Hidden Markov Modeling of Proteins |
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hmm |
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Week 8 |
MIDTERM EXAM |
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Week 9 |
Microarray and related technologies |
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Week 10 |
Gene Expression Analysis |
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Week 11 |
Network Analysis and Diseases |
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4 Dec. |
Data-Driven View of Disease Biology |
Berkay |
PLOS CB |
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Protein Interactions and Disease |
Levent |
PLOS CB |
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Network Biology Approach to Complex Diseases |
Ahmet |
PLOS CB |
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Week 12 |
Biological Knowledge Discovery & Management |
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11 Dec. |
Pharmacogenomics |
Serkan |
PLOS CB |
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Biological Knowledge Assembly and Interpretation |
Erhan |
PLOS CB |
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Analyses Using Disease Ontologies |
Berke |
PLOS CB |
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Week 13 |
Other Data in Clinical Applications |
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17 Dec. |
Mining Genome-Wide Genetic Markers |
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PLOS CB |
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Text Mining for Translational Bioinformatics |
Deniz |
PLOS CB |
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Bioimage Informatics for Systems Pharmacology |
Gökhan |
PLOS CB |
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Week 14 |
Project Discussions |
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Announcements:
Grades
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