Fundamental Models and Algorithms in Bioinformatics
INFO I519 (= I617) Fall 2021
Course description
INFO I519 FMAB
Class times and locations
Mon, Wed 3:15p - 4:30p (Credits: 3.0); Lindley Hall (LH) 025
Computer Laboratory, Fri 9:25a - 10:40a; Radio-TV (TV) 186
Tentative schedule (click the icon for a 
version)
| DAY | DATE | LECTURE | TOPIC | LECTURER | Mon | Aug 23 | 1.1 | Orientation Topics in bioinformatics, scope of class, and resources Catch-up for non-life scientists: An introduction to DNA (Khan Academy) Module 1: Bioinformatics resources and workspacesNational Center for Biotechnology Information (NCBI), a great starting point for "anything" bioinformatics Ubuntu on Windows: ... a quick way to get to a command line terminal Virtual Machines: VirtualBox VMware | Volker Brendel |
| Wed | Aug 25 | 1.2 | Basic bioinformatics toolkit acquisition (Part I) NCBI E-Utilities ... slides Installing NCBI EDirect EDirect Sample Code Explained | Volker Brendel |
| Fri | Aug 27 | L1.1 | Computer Laboratory: Linux Basics Basic UNIX shell tutorial The UNIX Shell The UNIX Shell: Summary of Basic Commands vi(m) editor tutorial | Shivani Vogiral |
| Mon | Aug 30 | 1.3 | Mapping biological question onto computational problems: The modeling spiral Sequence gazing: the famous TATA-box | Volker Brendel |
| Wed | Sept 1 | 1.4 | Basic statistical questions in bioinformatics Quiz I | Volker Brendel |
| Fri | Sept 3 | L1.2 | Computer Laboratory: Basic bioinformatics toolkit acquisition (Part II): Getting code: git GitHub Brendel Group on GitHub GitHub HowTo git: working with branches CodeFMAB | Shivani Vogiral |
| Mon | Sept 6 | 2.1 | Module 2: Sequence Models and SpacesLabor Day | no class |
| Wed | Sept 8 | 2.2 | Simple Sequence Models | Volker Brendel |
| Fri | Sept 10 | L2.1 | Computer Laboratory: Python Basics Python tutorial Python Scripting for Computational Molecular Science Python for Everybody PY4E Lessons J. Sundnes: Introduction to Scientific Programming with Python Style matters ... Learning Scientific Programming with Python - an intriguing resource | Shivani Vogiral |
| Mon | Sept 13 | 2.3 | Markov Models for Sequences | Volker Brendel |
| Wed | Sept 15 | 2.4 | Applications of Markov Models GENMARK Some resources for statistics background review: Event probabilities Union of events Bayes Theorem Probability distribution Expected value Review: Conditional Probability Sensitity, specificity, and all that Stat225 at Purdue - nice slides by Dr. Whitney Huang Quiz II | Volker Brendel |
| Fri | Sept 17 | L2.1 | Computer Laboratory: Coding random sequence generation and pattern probability calculations | Shivani Vogiral |
| Mon | Sept 20 | 3.1 | Module 3: Pairwise Sequence AlignmentModels for Pairwise Sequence Alignment | Volker Brendel |
| Wed | Sept 22 | 3.2 | PWSA: #NW algorithm. | Volker Brendel |
| Fri | Sept 24 | L3.1 | Computer Laboratory: Coding #NW algorithm. | Shivani Vogiral |
| Mon | Sept 27 | 3.3 | Algorithms for Pairwise Sequence Alignment How Do We Compare Biological Sequences? (from Bioinformatics: An Active Learning Approach) | Volker Brendel |
| Wed | Sept 29 | 3.4 | PWSA: gSW, lSW, and other algorithms. | Volker Brendel |
| Fri | Oct 1 | L3.2 | Computer Laboratory: Coding PWSA algorithms. Quiz III to be posted as an assignment. | Shivani Vogiral |
| Mon | Oct 4 | 4.1 | Module 4: Sequence Analysis with ScoresSequence Analysis with Scores: Theory | Volker Brendel |
| Wed | Oct 6 | 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 8 | Fall Break: no class | ||
| Mon | Oct 11 | 4.3 | Sequence Analysis with Scores: Applications | Volker Brendel |
| Wed | Oct 13 | 4.4 | TBA Quiz IV | Volker Brendel |
| Fri | Oct 15 | L4.2 | Computer Laboratory: | Shivani Vogiral |
| Mon | Oct 18 | 5.1 | Module 5: Hidden Markov ModelsHidden Markov Models: Motivation Rabiner's Tutorial | Volker Brendel |
| Wed | Oct 20 | 5.2 | Hidden Markov Models: Algorithms Hidden Markov Models (from Bioinformatics: An Active Learning Approach) | Volker Brendel |
| Fri | Oct 22 | L5.1 | Computer Laboratory: Plotting functions and histograms and more with python | Shivani Vogiral |
| Mon | Oct 25 | 5.3 | Hidden Markov Models: Applications Application examples GENSCAN Profile Hidden Markov Models TagDust Tagdust2 on github | Volker Brendel |
| Wed | Oct 27 | 5.4 | Sequence motifs: algorithms InterPro The MEME Suite HOMER Quiz V posted | Volker Brendel |
| Fri | Oct 29 | L5.2 | Computer Laboratory: Implementation of HMM algorithms | Shivani Vogiral |
| Mon | Nov 1 | 6.1 | Module 6: Basic Concepts of Molecular PhylogeneticsMolecular Phylogeny: Models The powers and pitfalls of parsimony | Volker Brendel |
| Wed | Nov 3 | 6.2 | TBA | Volker Brendel |
| Fri | Nov 5 | L6.1 | Computer Laboratory: Molecular Phylogeny, applications | Shivani Vogiral |
| Mon | Nov 8 | 6.3 | Molecular Phylogeny: Applications Lectures on molecular phylogeny (from Bioinformatics: An Active Learning Approach) | Volker Brendel |
| Wed | Nov 10 | 6.4 | TBA Quiz VI | Volker Brendel |
| Fri | Nov 12 | L6.2 | Computer Laboratory: | Shivani Vogiral |
| Mon | Nov 15 | 7.1 | Module 7: Genome Assembly and AnnotationDNA Sequencing Sanger sequencing Illumina sequencing nanopore sequencing Genome Resources The Genomic Landscape circa 2016 (Lecturer: Dr. Andy Green) Assembly basics NCBI Assembly Help NCBI Genome Genome Assembly Introduction to genome sequencing How do we assemble genomes? from Bioinformatics Algorithms: An Active Learning Approach | Volker Brendel |
| Wed | Nov 17 | 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 Project Assignment Posted | Volker Brendel |
| Fri | Nov 19 | L7.1 | Computer Laboratory: | Shivani Vogiral |
| Mon | Nov 23 | THANKSGIVING BREAK | n/a | |
| Wed | Nov 25 | THANKSGIVING BREAK | n/a | |
| Fri | Nov 27 | THANKSGIVING BREAK | n/a | |
| Mon | Nov 29 | 8.1 | Module 8: Genetic VariationGenetic variation Interpreting an individual genome NCBI dbSNP How To NCBI dbVar How To 1000 Genomes Project Nature 491:56 Example: rs1131769 file format specifications: Variant Call Format (VCF) Sequence Alignment Map format (SAM) SAM flags explained Pileup format (used by samtools) Relevant code: NCBI SRA Toolkit samtools bwa freebayes | Volker Brendel |
| Wed | Dec 1 | 9.1 | Module 9: Protein Structurepeptide bond Ramachandran plot ... very nice visualization thereof (thanks to Prof. Eric Martz) PDB: What is a protein? PDB: How enzymes work HIV I HIV II Guide to PDB PDB Molecule of the Month NCBI Protein Secondary Structure 2struct server Jpred - secondary structure prediction SPIDER3 foldit AlphaFold | Volker Brendel |
| Fri | Dec 3 | L7.2 | Computer Laboratory: wgsim - read generator SoapDeNovo2 - assembler Project Assignment Due | Shivani Vogiral |
| Mon | Dec 6 | Review SessionsSequence Alignment Bioinformatics Algorithms presentation | Volker Brendel | |
| Wed | Dec 8 | Gene Expression Analyses from Bioinformatics Algorithms: An Active Learning Approach MIT Lecture: Gene Regulatory Networks MIT Data Science: Clustering | Volker Brendel | |
| Fri | Dec 10 | Zoom office hour | Shivani Vogiral | |
| Mon | Dec 13 | 12:35 - 2:35pm | Final Examination | Students |