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<h1>CSE 6153: Computational Biology and Bioinformatics</h1>
<p><b>Summer 2016</b></p>
<b>Course Teacher</b> <br>
Dr. Swakkhar Shatabda<br>
Assistant Professor & Undergraduate Program Coordinator<br>
Department of CSE, United International University <br>
Room: 104 Email: swakkhar@cse.uiu.ac.bd Phone: 01776195310<br>
<p>
<b>Class Time</b><br>
Friday, 3:30PM - 6:30 PM Room # 105
<br>
<p><b>Books</b><br>
1. Introduction to Bioinformatics Algorithms
<a href="https://www.dropbox.com/s/c5kbg4lemq6t29k/introduction.to.bioinformatics.algorithms.pdf?dl=0"> download link </a> <br>
2. Cartoon Guide to Genetics
<a href="https://drive.google.com/open?id=0B8PVD2E6RiteRXlHX0pmbVJqZW8"> download link </a> <br>
<p><b>Course Schedule</b> <br>
Week 1: Molecular Biology Primer <a href="http://www.math.ucsd.edu/~pcompeau/Ch03_Molecular_Biology_Primer_Edited.pdf">slides</a> <br>
Week 2: Genome Assembly <a href="http://www.nature.com/nbt/journal/v29/n11/full/nbt.2023.html">paper</a> <a href="https://www.dropbox.com/s/o5wjugo7v04lmm1/genomeassembly.pdf?dl=0">slides</a><br>
Week 3: Finding Hidden Messages <a href="http://nar.oxfordjournals.org/content/32/13/3781.full">paper</a> <a href="https://www.dropbox.com/s/q5ityvdqksfjia7/hiddenmsg.pdf?dl=0">slides</a> <a href="https://docs.google.com/presentation/d/19VKjFeFck0YHcvZuR6oR-Gy1qm2E46Kua9j7ZU5qAaw/edit?usp=sharing">Presentation by Jayed</a><br>
Week 4: Peptide Sequencing <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3216106/pdf/cmb.2011.0158.pdf">paper</a> <a href="https://www.dropbox.com/s/2w3ksxt0k2dh865/pesptides.pdf?dl=0">slides</a> <br>
Week 5: Structure Prediction <a href="https://www.dropbox.com/s/4w5v8nm66kwla98/dotu2011.pdf?dl=0">paper</a> <a href="https://www.dropbox.com/s/cm2b7v27mlvv5mj/structures.pdf?dl=0">sides</a><br>
Week 6: Genome Rearrangement <a href="https://www.dropbox.com/s/jd2vzseqctrxgev/Ch05_Rearrangements_Edited.pdf?dl=0">slides</a> <a href="http://teacher.buet.ac.bd/saidurrahman/walcom2007/proceedings/arahman.pdf">paper</a> <br>
Week 7: Clustering <a href="https://www.dropbox.com/s/8vbxsow1xa1glgn/Ch10_Clustering_Edited.ppt?dl=0">slides</a> <br>
Week 8: Only Presentations <br>
Week 9: Hidden Markov Models <a href="https://www.dropbox.com/s/bxme9fmwvdrt63m/Ch11_HMM_Edited.ppt?dl=0"> slides </a> <br>
Week 10: Phylogeny <br>
Week 11: Sequence Alignment <br>
Week 12: Machine Learning Algorithms <br>
<p><b>Grading</b><br>
1. Class Attendance - 10%<br>
2. Project (presentation+report) - 20% + 30%<br>
3. Final Exam - 40%<br>
Sample question <a href="https://www.dropbox.com/s/d4uz9grxac98q2q/midexam01.pdf?dl=0"> mid </a> <a href="https://www.dropbox.com/s/pfqrppwitp5imr8/finalexam01.pdf?dl=0"> final </a>
<p><b>Topics for Project/Report</b><br>
1. Read papers () <br>
2. Run Experiments (BLAST, UCI, PDB, GenBank, etc) <br>
<p> How to read a scientific paper? <a href="https://www.elsevier.com/connect/infographic-how-to-read-a-scientific-paper">infographic</a><br>
<p><a href="https://www.dropbox.com/s/1ysdvyxx498660w/00.ten%20rules%20for%20literature%20review.pdf?dl=0">10 rules for literature review</a><br>
<p><a href="https://www.dropbox.com/s/xmujqi5uabxe1l0/00.%20why.pdf?dl=0">Why you want to be a computational biologist?</a><br>
A sample report <a href="https://www.dropbox.com/s/s463p4l5l8cnna0/reprotCBB.pdf?dl=0"> report.pdf </a>
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