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

BIOL-L/MLS-M 388 Spring 2021


Course description

BIOL L388 DB

Class times and locations

Tues, Thur 11:30a - 12:45p (Credits: 3.0); online / Psychology (PY) 100

Tentative schedule (class notes can be viewed with Adobe Acrobat Reader)

HTML version of this schedule











DAYDATELECTURETOPICLECTURER
Tues Jan 19 0.1 Orientation
What is Digital Biology?

Motivation
Current Topics in Genome Analysis 2016, a National Human Genome Research Institute lecture series:
The Genomic Landscape circa 2016 (Lecturer: Dr. Andy Green)

MIT Lectures on "COVID-19, SARS-CoV-2 and the Pandemic"

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
Volker Brendel
Thur Jan 21 1.1 Bioinformatics Skills

Basic UNIX shell tutorial
Command-line bootcamp
vi(m) editor tutorial

Python tutorial
Style matters ...
Learning Scientific Programming with Python - an intriguing resource
Volker Brendel
Tues Jan 26 1.2 Mapping biological question onto computational problems:
The modeling spiral

Sequence gazing: the famous TATA-box

Sequence Spaces and Models

Customizing your Bioinformatics Toolbox
Virtual Machines: VirtualBox VMware
Getting code: git GitHub Brendel Group on GitHub
CodeFMAB
Volker Brendel
Thur Jan 28 1.3 Review of Module 1

Quiz 1
Students
Tues Feb 2 2.1 Sequence Alignments 1

How Do We Compare Biological Sequences?
from Bioinformatics Algorithms: An Active Learning Approach



Some presentations for further study:

Biological Sequence Analysis I (Lecturer: Dr. Andy Baxevanis
Biological Sequence Analysis II (Lecturer: Dr. Andy Baxevanis)
Volker Brendel
Thur Feb 4 2.2 Sequence Alignments 2
MIT video: Local Alignment (BLAST) and Statistics
Volker Brendel
Tues Feb 9 2.3 Sequence Alignments 3
MIT video: Global Alignment of Protein Sequences (NW,SW, PAM, BLOSUM)
Volker Brendel
Thur Feb 11 2.4 Sequence analysis with scores: Substitution scoring matrices
Biological Sequence Analysis I (Lecturer: Dr. Andy Baxevanis)

Slides for Sequence Analysis I presentation
Handout for Sequence Analysis I presentation

Quiz 2
Volker Brendel

Students
Tues Feb 16 3.3 Wellness Day no class
Thur Feb 18 3.2

Evolutionary Processes 1

Introduction to Molecular Evolution
The Fastest Outbreak
Transforming Distance Matrices into Evolutionary Trees
Toward an Algorithm for Distance-Based Phylogeny Construction
Additive Phylogeny
Using Least-Squares To Construct Distance-Based Phylogenies
Ultrametric Trees
The Neighbor-Joining Algorithm

The powers and pitfalls of parsimony

Evolutionary Processes 2

Character-based Tree Reconstruction
The Small Parsimony Problem
The Large Parsimony Problem
Evolutionary Tree Reconstruction in the Modern Era
Volker Brendel
Tues Feb 23 3.3 Evolutionary Processes 3

GBE article on lungfish development

EBI MSA Tools
EBI MP Tools

... a bit of history
Volker Brendel
Thur Feb 25 3.4 Quiz 3 Students
Tues Mar 2 4.1 Genome Characteristics 1 (Motivation)

The Genomic Landscape circa 2016 (Lecturer: Dr. Andy Green)

Assembly basics
NCBI Genome

Genome Characteristics 2 (Assembly)

Introduction to genome sequencing
How do we assemble genomes?
from Bioinformatics Algorithms: An Active Learning Approach
Volker Brendel
Thur Mar 4 4.2 Genome Characteristics 2 (Assembly) ... continued

Sanger sequencing
Illumina sequencing
nanopore sequencing
Volker Brendel
Tues March 9 4.3 Genome Characteristics 3 (Assembly) ... continued

NCBI Assembly Help
paper wasp genome page
Other types of assembly: RNA-Seq
Volker Brendel
Thur March 11 4.4 Genome Annotation: Introduction

Eufriesea mexicana genome page at NCBI
GFF3 standard
tRNAscan-SE

Quiz 4
Volker Brendel

Students
Tues March 16 5.1 Genome Annotation: Models

Review: Conditional Probability

Hidden Markov Models: Concepts and Algorithms

Hidden Markov Models
(from Bioinformatics: An Active Learning Approach)

GeneMark (old article from the early days)
GENSCAN
Profile Hidden Markov Models
TagDust
Volker Brendel
Thur March 18 5.2 Genome Annotation: Practice

GeneMark.hmm prokaryotic
GeneMark.hmm eukaryotic
AUGUSTUS
GENSCAN

Volker Brendel
Tues March 23 5.3 Genome Annotation: Evaluation

Sensitivity, specificity, and all that
sample paper

How to evaluate gene structure prediction accuracy

Volker Brendel
Thur March 25 6.1 Protein Structures 1
PDB: What is a protein?
PDB: How enzymes work
HIV I
HIV II

Guide to PDB

PDB Molecule of the Month
NCBI Protein

MIT Lecture: Introduction to Protein Structure; Structure Comparison and Classification
Volker Brendel
Tues March 30 6.2 Protein Structures 2

peptide bond
Ramachandran plot ... very nice visualization thereof
(thanks to Prof. Eric Martz)

foldit
AlphaFold

MIT Lecture: Predicting Protein Structure
Online Class
Volker Brendel
Thur April 1 6.3 Protein Structures 3: Secondary Structure

2StruCompare server

Jpred - secondary structure prediction
SPIDER3

HMMer
PFAM

Quiz 5
Volker Brendel

Students
Tues April 6 7.1 Genetic variation
Interpreting an individual genome

NCBI dbSNP    How To
NCBI dbVar    How To
1000 Genomes Project    Nature 491:56
Example: rs1131769
Recent paper of interest
Volker Brendel
Thur April 8 7.2 Relevant 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
Thur April 13 7.3 Gene Expression Analyses
from Bioinformatics Algorithms: An Active Learning Approach

MIT Lecture: Gene Regulatory Networks
MIT Data Science: Clustering
Volker Brendel
Thur April 15 7.4 Quiz 6 Students
Tues April 20 7.5 Volker Brendel
Thur April 22 Wellness Day no class
Tues April 27 8.1 Review
Volker Brendel
Thur April 29 8.2 Review
Volker Brendel
Thur May 6 7:45am - 9:45am

PY 100
Final Examination Students