Digital Biology: A survey of topics in bioinformatics and functional genomics

BIOL-L/MLS-M 388 Spring 2023

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Course description

BIOL L388 DB

Class times and locations

Tues, Thur 11:30a - 12:45p (Credits: 3.0); Swain East (SE) 010

version of this schedule

DAY	DATE	LECTURE	TOPIC	LECTURER
Tues	Jan 10	0.1	Orientation What is Digital Biology? Topics in bioinformatics, scope of class, and resources Motivation New virus outbreak: BBC Jan. 19, 2020 New virus outbreak: BBC Jan. 20, 2020 2023: XBB.1.5 NCBI SARS-CoV-2 Precedence: The Fastest Outbreak - connection to bioinformatics work Bioinformatics Databases and Computing Resources National Center for Biotechnology Information (NCBI), a great starting point for "anything" bioinformatics Mapping biological question onto computational problems: The modeling spiral Sequence gazing: the famous TATA-box AlphaFold	Volker Brendel
Thur	Jan 12	1.1	Module 1: Bioinformatics resources and workspaces Ubuntu on Windows: ... a quick way to get to a command line terminal Virtual Machines: VirtualBox Linux Basics Basic UNIX shell tutorial Command-line bootcamp The UNIX Shell The UNIX Shell: Summary of Basic Commands vi(m) editor tutorial	Volker Brendel
Tues	Jan 17	1.2	Customizing your Linux work space Getting code with git Working with NCBI data	Volker Brendel
Thur	Jan 19	1.3	Command line access to NCBI data: EDirect Entrez Direct NCBI Sequence search fields MEDLINE/PubMed search fields	Volker Brendel
Tues	Jan 24	1.4	Review: Command-line bootcamp	Volker Brendel
Thur	Jan 26	1.5	Review: Statistical evaluation of sequence features Using generic Linux commands to process sequence data (at least for previews or consistency checks ...) Home Work Assignment 1 posted. Due: Feb. 2, 6:00pm	Volker Brendel
Tues	Jan 31	2.1	Module 2: Pairwise Sequence Alignment Motivation How Do We Compare Biological Sequences? from Bioinformatics Algorithms: An Active Learning Approach	Volker Brendel
Thur	Feb 2	2.2	PWSA: Definition and representation of "alignments" Home Work Assignment 1 due at 6:00pm	Volker Brendel
Tues	Feb 7	2.3	Global alignment (Needleman-Wunsch) How to calculate the number of NW alignments	Volker Brendel
Thur	Feb 9	2.4	Scoring alignments How to calculate the optimal alignment score (and find an optimal alignment) PWSA: allowing "double-gaps" PWSA: local alignment (Smith-Waterman) Home Work Assignment 2 posted. Due: Feb. 17, 6:59pm	Volker Brendel
Tues	Feb 14	2.5	Sequence analysis with scores: Concepts and statistical foundations	Volker Brendel
Thur	Feb 16	2.6	Sequence analysis with scores: Practice BLAST and Substitution scoring matrices Biological Sequence Analysis I (Lecturer: Dr. Andy Baxevanis) Slides for Sequence Analysis I presentation Handout for Sequence Analysis I presentation	Volker Brendel
Tues	Feb 21	3.1	Module 3: Basic Concepts in Molecular Phylogenetics Molecular Phylogeny: Models The powers and pitfalls of parsimony	Volker Brendel
Thur	Feb 23	3.2	Lectures on molecular phylogeny (from Bioinformatics: An Active Learning Approach)	Volker Brendel
Tues	Feb 28	3.3	Methods I: Parsimony Home Work Assignment 3 posted. Due: March 7, 11:00pm	Volker Brendel
Thur	March 2	3.4	Methods II: Distance matrix methods	Volker Brendel
Tues	March 7	4.1	Module 4: Hidden Markov Models Hidden Markov Models: Concepts and Algorithms Hidden Markov Models (from Bioinformatics: An Active Learning Approach)	Volker Brendel
Thur	March 9	4.2	Hidden Markov Models: Applications Profile Hidden Markov Models TagDust Tagdust2 on github GeneMark.hmm prokaryotic GENSCAN; paper see here Background: GeneMark article Review: Conditional Probability	Volker Brendel
Tues	March 14		Spring Break
Thur	March 16		Spring Break
Tues	March 21	5.1	Module 5: Genome Assembly and Annotation Eukaryotic gene finding: GeneMark AUGUSTUS	Volker Brendel
Thur	March 23	5.2	Genome Annotation: Evaluation Sensitivity, specificity, and all that sample paper How to evaluate gene structure prediction accuracy	Volker Brendel
Tues	March 28	5.3	Genome Sequencing: Illumina sequencing nanopore sequencing Assembly basics NCBI Assembly Help	Volker Brendel
Thur	March 30	5.4	Genome assembly: How do we assemble genomes? from Bioinformatics Algorithms: An Active Learning Approach	Volker Brendel
Tues	April 4	6.1	Module 6: Genetic Variation Home Work Assignment 5 posted. Due: April 11, 7:00pm Home Work Assignment 6 posted. Due: April 14, 11:00pm	Volker Brendel
Thur	April 6	6.2	Sequence Alignment Map format (SAM) SAM flags explained Pileup format (used by samtools) Relevant code: samtools bwa	Volker Brendel
Tues	April 11	6.3	Relevant file format specifications: Variant Call Format (VCF) Relevant code: NCBI SRA Toolkit freebayes	Volker Brendel
Thur	April 13	6.4	Gene Expression Analyses from Bioinformatics Algorithms: An Active Learning Approach MIT Lecture: Gene Regulatory Networks MIT Data Science: Clustering	Volker Brendel
Tues	April 18	7.1	Module 7: Protein Structure PDB: What is a protein? PDB: How enzymes work Guide to PDB PDB Molecule of the Month NCBI Protein	Volker Brendel
Thur	April 20	7.2	peptide bond Ramachandran plot ... very nice visualization thereof (thanks to Prof. Eric Martz) Secondary Structure 2StruCompare server Jpred - secondary structure prediction SPIDER3 HMMer PFAM foldit AlphaFold	Volker Brendel
Tues	April 25	8.1	Review: Managing workflows loops in bash	Volker Brendel
Thur	April 27	8.2	Review	Volker Brendel
Thur	May 4	12:20pm	Final Project submission due	Students