Fundamental Models and Algorithms in Bioinformatics
INFO I519 (= I617) Fall 2017
Course description
INFO I519 FMAB
Class times and locations
Mon, Wed 2:30p - 3:45p; Informatics West (I) 107
Computer Laboratory, Fri 8:00a-9:15a, Ballentine Hall (JH) 308
Tentative schedule (click the icon for a 
version)
| DAY | DATE | LECTURE | TOPIC | LECTURER |
| Mon | Aug 21 | 0.1 | Orientation Introduction: Topics in bioinformatics, scope of class, and resources Mapping biological question onto computational problems: The modeling spiral 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 23 | 0.2 | Computer Laboratory: Basic bioinformatics toolkit acquisition I Setting up Linux virtual machines VirtualBox Linux Mint How to Install Linux Mint 18 Cinnamon on VirtualBox Step by Step | Murat Öztürk & Volker Brendel |
| Fri | Aug 25 | Computer Laboratory: Basic bioinformatics toolkit acquisition II Basic UNIX Shell Tutorial Command-line bootcamp Python tutorial Style matters ... | Murat Öztürk | |
| Mon | Aug 28 | 1.1 | Simple sequence models | Volker Brendel |
| Wed | Aug 30 | 1.2 | Advanced sequence models and applications | Volker Brendel |
| Fri | Sept 1 | Computer Laboratory: Linux Basics | Murat Öztürk | |
| Mon | Sept 4 | No class (Labor Day) | ||
| Wed | Sept 6 | 0.1 - 1.2 | Quiz I | |
| Fri | Sept 8 | Computer Laboratory: | Murat Öztürk | |
| Mon | Sept 11 | 2.1 | Pairwise sequence alignment: Representation | Volker Brendel |
| Wed | Sept 13 | 2.2 | Pairwise sequence alignment: Basic algorithms | Volker Brendel |
| Fri | Sept 15 | Computer Laboratory: | Murat Öztürk | |
| Mon | Sept 18 | 2.3 | Pairwise sequence alignment: Applications How Do We Compare Biological Sequences? (from Bioinformatics: An Active Learning Approach) | Volker Brendel |
| Wed | Sept 20 | 2.4 | Multiple sequence alignment | Volker Brendel |
| Fri | Sept 22 | Computer Laboratory: | Murat Öztürk | |
| Mon | Sept 25 | 2.1 - 2.4 | Quiz II | |
| Wed | Sept 26 | 3.1 | Applications of Markov Models: Pattern probabilities | Volker Brendel |
| Fri | Sept 29 | Computer Laboratory: | Murat Öztürk | |
| Mon | Oct 2 | 4.1 | Sequence analysis with scores: Concepts and Applications NCBI BLAST | Volker Brendel |
| Wed | Oct 4 | 4.2 | Sequence analysis with scores: Substitution scoring matrices | Volker Brendel |
| Fri | Oct 6 | Fall Break: no class | ||
| Mon | Oct 9 | 4.3 | BLAST: Fine points of database searching | Volker Brendel |
| Wed | Oct 11 | 3.1 | Hidden Markov Models: Concepts and Algorithms Hidden Markov Models (from Bioinformatics: An Active Learning Approach) | Volker Brendel |
| Fri | Oct 13 | Computer Laboratory: | Thomas McCarthy | |
| Mon | Oct 16 | 3.2 | Hidden Markov Models: Applications Application examples GENSCAN Profile Hidden Markov Models TagDust | Volker Brendel |
| Wed | Oct 18 | 3.1 - 4.3 | Quiz III | |
| Fri | Oct 20 | Computer Laboratory: | Murat Öztürk | |
| Mon | Oct 23 | 5.1 | Sequence motifs: models Biological Sequence Analysis II (Lecturer: Dr. Andy Baxevanis) Pfam | Volker Brendel |
| Wed | Oct 25 | 5.2 | Sequence motifs: algorithms InterPro The MEME Suite HOMER | Volker Brendel |
| Fri | Oct 27 | Computer Laboratory: | Murat Öztürk | |
| Mon | Oct 30 | 6.1 | Molecular Phylogeny: concepts The powers and pitfalls of parsimony | Volker Brendel |
| Wed | Nov 1 | 6.2 | Molecular Phylogeny: algorithms a recent paper ... A list of Web-servers for molecular phylogeny analyses phylogeny.fr | Volker Brendel |
| Fri | Nov 3 | Computer Laboratory: Molecular Phylogeny, applications | Murat Öztürk | |
| Mon | Nov 6 | 6.3 | Molecular Phylogeny: details Lectures on molecular phylogeny (from Bioinformatics: An Active Learning Approach) | Volker Brendel |
| Wed | Nov 8 | 7.1 | Protein bioinformatics: structure prediction Nobel Price lecture 2013: Michael Levitt 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 10 | Computer Laboratory: | Murat Öztürk | |
| Mon | Nov 13 | 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 15 | 5.1 - 7.2 | Quiz IV | |
| Fri | Nov 17 | Computer Laboratory: | Murat Öztürk | |
| Mon | Nov 20 | THANKSGIVING BREAK | n/a | |
| Wed | Nov 22 | THANKSGIVING BREAK | n/a | |
| Fri | Nov 24 | THANKSGIVING BREAK | n/a | |
| Mon | Nov 27 | 8.1 | Genome assembly I: algorithms Bioinformatics Algorithms: An Active Learning Approach (Chapter 3); see Bioinformatics Algorithms a (personal) historical note ... | Volker Brendel |
| Wed | Nov 29 | 8.2 | Genome assembly II: practice Overview of sequencing technologies Illumina | Volker Brendel |
| Fri | Dec 1 | Computer Laboratory: wgsim - read generator SoapDeNovo2 - assembler | Murat Öztürk | |
| Mon | Dec 4 | 9.1 | Review I: Sequence Alignment Bioinformatics Algorithms presentation | Volker Brendel |
| Wed | Dec 6 | Review | Volker Brendel | |
| Fri | Dec 8 | Computer Laboratory: | Murat Öztürk | |
| Mon | Dec 11 | 12:30 - 2:30pm | Final Exam | Students |