Digital Biology: A survey of topics in bioinformatics and functional genomics
BIOL L388 (offered as L410) Spring 2017
Course description
BIOL L388 DB
Class times and locations
Tues, Thur 11:15a - 12:30p (Credits: 3.0); Global & International Studies (GA) 0013
Tentative schedule (click the icon for a 
version)
| DAY | DATE | LECTURE | TOPIC | LECTURER | Tues | Jan 10 | 0.1 | Orientation What is Digital Biology? MIT video: Introduction to Computational and Systems Biology | Volker Brendel |
| Thur | Jan 12 | 1.1 | Review: Nucleic Acids and Proteins | Volker Brendel |
| Tues | Jan 17 | 1.2 | Bioinformatics Databases and Computing Resources National Center for Biotechnology Information (NCBI), a great starting point for "anything" bioinformatics Current Topics in Genome Analysis 2016, a National Human Genome Research Institute lecture series: The Genomic Landscape circa 2016 (Lecturer: Dr. Andy Green) Biological Sequence Analysis I (Lecturer: Dr. Andy Baxevanis Biological Sequence Analysis II (Lecturer: Dr. Andy Baxevanis) | Volker Brendel |
| Thur | Jan 19 | 1.3 | Quiz 1 | Students |
| Tues | Jan 24 | 2.1 | Sequence Alignments 1 How Do We Compare Biological Sequences? from Bioinformatics Algorithms: An Active Learning Approach | Volker Brendel |
| Thur | Jan 26 | 2.2 | Sequence Alignments 2 MIT video: Local Alignment (BLAST) and Statistics | Volker Brendel |
| Tues | Jan 31 | 2.3 | Sequence Alignments 3 MIT video: Global Alignment of Protein Sequences (NW,SW, PAM, BLOSUM) | Volker Brendel |
| Thur | Feb 2 | 2.4 | Quiz 2 | Students |
| Tues | Feb 7 | 3.1 | Evolutionary Processes 1 Introduction to Molecular Evolution The Fastest Outbreak Transforming Distance Matrices into Evolutionary Trees Toward an Algorithm for Distance-Based Phylogeny Construction Additive Phylogeny Using Least-Squares To Construct Distance-Based Phylogenies Ultrametric Trees The Neighbor-Joining Algorithm | Volker Brendel |
| Thur | Feb 9 | 3.2 | Evolutionary Processes 2 Character-based Tree Reconstruction The Small Parsimony Problem The Large Parsimony Problem Evolutionary Tree Reconstruction in the Modern Era | Volker Brendel |
| Tues | Feb 14 | 3.3 | Evolutionary Processes 3 | Volker Brendel |
| Thur | Feb 16 | 3.4 | Quiz 3 | Students |
| Tues | Feb 21 | 4.1 | Genome Characteristics 1 PDB Molecule of the Month NCBI Protein EBI MSA Tools EBI MP Tools | Volker Brendel |
| Thur | Feb 23 | 4.2 | Genome Characteristics 2 | Volker Brendel |
| Tues | Feb 28 | 4.3 | DNA/RNA Sequencing: Principles and Practice Class meets in Myers Hall 140 | Dr. James Ford |
| Thur | March 2 | 4.4 | Introduction to genome sequencing How do we assemble genomes? from Bioinformatics Algorithms: An Active Learning Approach Quiz 4 | Students |
| Tues | March 7 | 5.1 | Genome Assembly | Volker Brendel |
| Thur | March 9 | 5.2 | Genome Annotation GeneMark AUGUSTUS | Volker Brendel |
| Tues | March 14 | Spring Break | ||
| Thur | March 16 | Spring Break | ||
| Tues | March 21 | 5.3 | Secondary Structures MIT Lecture: Introduction to Protein Structure; Structure Comparison and Classification | Volker Brendel |
| Thur | March 23 | 5.4 | Quiz 5 | Students |
| Tues | March 28 | 6.1 | Tertiary Structures 1 MIT Lecture: Predicting Protein Structure | Volker Brendel |
| Thur | March 30 | 6.2 | Tertiary Structures 2 MIT Lecture: Predicting Protein Interactions | Volker Brendel |
| Tues | April 4 | 6.3 | Tertiary Structures 3 foldit | Volker Brendel |
| Thur | April 6 | 6.4 | Quiz 6 | Students |
| Tues | April 11 | 7.1 | Cells and Organisms 1 | Volker Brendel |
| Thur | April 13 | 7.2 | Cells and Organisms 2 | Volker Brendel |
| Tues | April 18 | 7.3 | Cells and Organisms 3 MIT Lecture: Gene Regulatory Networks | Volker Brendel |
| Thur | April 20 | 7.4 | Cells and Organisms 4 Course Questionnaire | Volker Brendel |
| Tues | April 25 | 8.1 | Review | Volker Brendel |
| Thur | April 27 | 8.2 | Review Gene Expression Analyses from Bioinformatics Algorithms: An Active Learning Approach | Volker Brendel |
| Thur | May 4 | 10:15am - 12:15pm | Final Examination | Students |