Fundamental Models and Algorithms in Bioinformatics
INFO I519 (= I617) Fall 2016
Course description
INFO I519 FMAB
Class times and locations
Mon, Wed 9:30a-10:45a, Ballentine Hall (BH) 305
Computer Laboratory, Fri 9:30a-10:45a, Jordan Hall (JH) 248
Tentative schedule (click the icon for a 
version)
| DAY | DATE | LECTURE | TOPIC | LECTURER |
| Mon | Aug 22 | 0.1 | Orientation Introduction: Topics in bioinformatics, scope of class, and resources Catch-up for non-life scientists: An introduction to DNA (Khan Academy) 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 |
| Wed | Aug 24 | 0.2 | Mapping biological question onto computational problems: The modeling spiral | Volker Brendel |
| Fri | Aug 26 | Computer Laboratory: Setting up Linux virtual machines VirtualBox Linux Mint How to Install Linux Mint 18 Cinnamon on VirtualBox Step by Step Basic UNIX Shell Tutorial | Murat Öztürk | |
| Mon | Aug 29 | 1.1 | Simple sequence models | Volker Brendel |
| Wed | Aug 31 | 1.2 | Advanced sequence models and applications | Volker Brendel |
| Fri | Sept 2 | Computer Laboratory: Linux Basics | Murat Öztürk | |
| Mon | Sept 5 | No class (Labor Day) | ||
| Wed | Sept 7 | 0.1 - 1.2 | Quiz I | |
| Fri | Sept 9 | Computer Laboratory: | Murat Öztürk | |
| Mon | Sept 12 | 2.1 | Pairwise sequence alignment: Representation | Volker Brendel |
| Wed | Sept 14 | 2.2 | Pairwise sequence alignment: Basic algorithms | Volker Brendel |
| Fri | Sept 16 | Computer Laboratory: | Murat Öztürk | |
| Mon | Sept 19 | 2.3 | Pairwise sequence alignment: Applications | Volker Brendel |
| Wed | Sept 21 | 2.4 | Multiple sequence alignment | Volker Brendel |
| Fri | Sept 23 | Computer Laboratory: | Murat Öztürk | |
| Mon | Sept 26 | 2.1 - 2.4 | Quiz II | |
| Wed | Sept 28 | 3.1 | Applications of Markov Models: Pattern probabilities | Volker Brendel |
| Fri | Sept 30 | Computer Laboratory: | Murat Öztürk | |
| Mon | Oct 3 | 3.2 | Hidden Markov Models: Concepts | Volker Brendel |
| Wed | Oct 5 | 3.3 | Hidden Markov Models: Algorithms | Volker Brendel |
| Fri | Oct 7 | Fall Break: no class | ||
| Mon | Oct 10 | Computer Laboratory: | Murat Öztürk | |
| Wed | Oct 12 | 3.4 | Hidden Markov Models: Applications Application examples GENSCAN Profile Hidden Markov Models TagDust | Volker Brendel |
| Mon | Oct 17 | 4.2 | Sequence analysis with scores: Concepts and Applications NCBI BLAST | Volker Brendel |
| Wed | Oct 19 | 3.1 - 4.2 | Quiz III | |
| Fri | Oct 21 | Computer Laboratory: | Murat Öztürk | |
| Mon | Oct 24 | 5.1 | Sequence motifs: models | Volker Brendel |
| Wed | Oct 26 | 5.2 | Sequence motifs: algorithms InterPro The MEME Suite HOMER | Volker Brendel |
| Fri | Oct 28 | Computer Laboratory: | Murat Öztürk | |
| Mon | Oct 31 | 6.1 | Molecular Phylogeny: concepts | Volker Brendel |
| Wed | Nov 2 | 6.2 | Molecular Phylogeny: algorithms A list of Web-servers for molecular phylogeny analyses Mobyle @ Pasteur BMPS Tutorial | Volker Brendel |
| Fri | Nov 4 | Computer Laboratory: | Murat Öztürk | |
| Mon | Nov 7 | 6.3 | Molecular Phylogeny: applications | Volker Brendel |
| Wed | Nov 9 | 7.1 | Protein bioinformatics: structure prediction RCSB PDB PDB-101 - a number of wonderful tutorials! SWISS-MODEL - what to do if my protein is not in PDB!? (start here) | Volker Brendel |
| Fri | Nov 11 | Computer Laboratory: | Murat Öztürk | |
| Mon | Nov 14 | 7.2 | Protein bioinformatics: structure analysis Genetic variation NCBI dbSNP How To NCBI dbVar How To 1000 Genomes Project Nature 491:56 Example: rs1131769 Recent paper of interest | Volker Brendel |
| Wed | Nov 16 | 5.1 - 7.2 | Quiz IV | |
| Fri | Nov 18 | Computer Laboratory: | Murat Öztürk | |
| Mon | Nov 21 | THANKSGIVING BREAK | n/a | |
| Wed | Nov 23 | THANKSGIVING BREAK | n/a | |
| Fri | Nov 25 | THANKSGIVING BREAK | n/a | |
| Mon | Nov 28 | 8.1 | Genome assembly: algorithms Bioinformatics Algorithms: An Active Learning Approach (Chapter 3); see Bioinformatics Algorithms a (personal) historical note ... | Volker Brendel |
| Wed | Nov 30 | 8.2 | Genome annotation | Volker Brendel |
| Fri | Dec 2 | Computer Laboratory: | Murat Öztürk | |
| Mon | Dec 5 | 9.1 | Review I: Sequence Alignment Bioinformatics Algorithms presentation | Volker Brendel |
| Wed | Dec 7 | Review | Volker Brendel | |
| Fri | Dec 9 | Computer Laboratory: | Murat Öztürk | |
| Mon | Dec 12 | 8:00am - 10:00am | Final Exam | Students |