Fundamental Models and Algorithms in Bioinformatics
INFO I519 (= I617) Fall 2020
Course description
INFO I519 FMAB
Class times and locations
Mon, Wed 3:15p - 4:30p; online
Computer Laboratory, Fri 9:25a-10:40a; online
Tentative schedule (click the icon for a 
version)
| DAY | DATE | LECTURE | TOPIC | LECTURER |
| Mon | Aug 24 | 1.1 | Orientation 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 NCBI E-Utilities ... slides Installing NCBI EDirect EDirect Sample Code Explained | Volker Brendel |
| Wed | Aug 26 | 1.2 | Basic bioinformatics toolkit acquisition (Part I) Basic UNIX shell tutorial The UNIX Shell The UNIX Shell: Summary of Basic Commands vi(m) editor tutorial | Volker Brendel |
| Fri | Aug 28 | L1.1 | Computer Laboratory Basic bioinformatics toolkit acquisition (Part II) Python tutorial Style matters ... Learning Scientific Programming with Python - an intriguing resource | Samer Al-Saffar |
| Mon | Aug 31 | 1.3 | Mapping biological question onto computational problems: The modeling spiral Sequence gazing: the famous TATA-box Customizing your Bioinformatics Toolbox Virtual Machines: VirtualBox VMware Getting code: git GitHub Brendel Group on GitHub CodeFMAB | Volker Brendel |
| Wed | Sept 2 | 1.4 | Basic statistical questions in bioinformatics Review: Conditional Probability Sensitity, specificity, and all that | Volker Brendel |
| Fri | Sept 4 | L1.2 | Computer Laboratory: Linux Basics | Samer Al-Saffar |
| Mon | Sept 7 | 2.1 | Sequence Spaces | Volker Brendel |
| Wed | Sept 9 | 2.2 | Simple Sequence Models | Volker Brendel |
| Fri | Sept 11 | L2.1 | Computer Laboratory: | Samer Al-Saffar |
| Mon | Sept 14 | 2.3 | Markov Models for Sequences GENMARK | Volker Brendel |
| Wed | Sept 16 | 2.4 | Applications of Markov Models Statistical Review: Event probabilities Union of events Bayes Theorem Probability distribution Expected value Stat225 at Purdue - nice slides by Dr. Whitney Huang | Volker Brendel |
| Fri | Sept 18 | L2.1 | Computer Laboratory: | Samer Al-Saffar |
| Mon | Sept 21 | 3.1 | Models for Pairwise Sequence Alignment | Volker Brendel |
| Wed | Sept 23 | 3.2 | TBA | Volker Brendel |
| Fri | Sept 25 | L3.1 | Computer Laboratory: | Samer Al-Saffar |
| Mon | Sept 28 | 3.3 | Algorithms for Pairwise Sequence Alignment | Volker Brendel |
| Wed | Sept 30 | 3.4 | TBA | Volker Brendel |
| Fri | Oct 2 | L3.2 | Computer Laboratory: | Samer Al-Saffar |
| Mon | Oct 5 | 4.1 | Sequence Analysis with Scores: Theory | Volker Brendel |
| Wed | Oct 7 | 4.2 | Sequence analysis with scores: Substitution scoring matrices Biological Sequence Analysis I (Lecturer: Dr. Andy Baxevanis) NCBI BLAST slides for Sequence Analysis I presentation handout for Sequence Analysis I presentation NCBI BLAST download site | Volker Brendel |
| Fri | Oct 9 | L4.1 | Computer Laboratory: | Samer Al-Saffar |
| Mon | Oct 12 | 4.3 | Sequence Analysis with Scores: Applications | Volker Brendel |
| Wed | Oct 14 | 4.4 | TBA | Volker Brendel |
| Fri | Oct 16 | L4.2 | Computer Laboratory | Samer Al-Saffar |
| Mon | Oct 19 | 5.1 | Hidden Markov Models: Theory Hidden Markov Models (from Bioinformatics: An Active Learning Approach) | Volker Brendel |
| Wed | Oct 21 | 5.2 | TBA | Volker Brendel |
| Fri | Oct 23 | L5.1 | Computer Laboratory: | Samer Al-Saffar |
| Mon | Oct 26 | 5.3 | Hidden Markov Models: Applications Application examples GENSCAN Profile Hidden Markov Models TagDust | Volker Brendel |
| Wed | Oct 28 | 5.4 | Sequence motifs: algorithms InterPro The MEME Suite HOMER | Volker Brendel |
| Fri | Oct 30 | L5.2 | Computer Laboratory: | Samer Al-Saffar |
| Mon | Nov 2 | 6.1 | Molecular Phylogeny: Models The powers and pitfalls of parsimony | Volker Brendel |
| Wed | Nov 4 | 6.2 | TBA | Volker Brendel |
| Fri | Nov 6 | L6.1 | Computer Laboratory: Molecular Phylogeny, applications | Samer Al-Saffar |
| Mon | Nov 9 | 6.3 | Molecular Phylogeny: Applications Lectures on molecular phylogeny (from Bioinformatics: An Active Learning Approach) | Volker Brendel |
| Wed | Nov 11 | 6.4 | TBA | Volker Brendel |
| Fri | Nov 13 | L6.2 | Computer Laboratory: | Samer Al-Saffar |
| Mon | Nov 16 | 7.1 | Topics in Bioinformatics Research 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 18 | 7.2 | Protein Structures RCSB PDB PDB: What is a protein? PDB: How enzymes work peptide bond Ramachandran plot ... very nice visualization thereof (thanks to Prof. Eric Martz) Guide to PDB PDB Molecule of the Month NCBI Protein Protein bioinformatics: structure prediction Nobel Price lecture 2013: Michael Levitt foldit | Volker Brendel |
| Fri | Nov 20 | L7.1 | Computer Laboratory: | Samer Al-Saffar |
| Mon | Nov 23 | THANKSGIVING BREAK | n/a | |
| Wed | Nov 25 | THANKSGIVING BREAK | n/a | |
| Fri | Nov 27 | THANKSGIVING BREAK | n/a | |
| Mon | Nov 30 | 7.3 | Topics in Bioinformatics Research: Protein Folding 2struct server Jpred - secondary structure prediction SPIDER3 CASP14 AlphaFold | Volker Brendel |
| Wed | Dec 2 | 7.4 | TBA | Volker Brendel |
| Fri | Dec 4 | L7.2 | Computer Laboratory: wgsim - read generator SoapDeNovo2 - assembler | Samer Al-Saffar |
| Mon | Dec 7 | Review I: Sequence Alignment Bioinformatics Algorithms presentation | Volker Brendel | |
| Wed | Dec 9 | Review II | Volker Brendel | |
| Fri | Dec 11 | Computer Laboratory: | Samer Al-Saffar | |
| Dec 18 | 2:30pm | Final Project Report due | Students |