| DAY | DATE | LECTURE | TOPIC | LECTURER |
Tues | Jan 14 | 0.1 | Orientation
What is Digital Biology?
MIT video: Introduction to Computational and Systems Biology | Volker Brendel |
| Thur | Jan 16 | 1.1 | 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 21 | 1.2 | New virus outbreak: BBC Jan. 19, 2020
New virus outbreak: BBC Jan. 20, 2020
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
Some presentations for further study:
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 |
| Thur | Jan 23 | 1.3 | codons and amino acids
amino acids
Quiz 1
... the hunt for a cure of Huntington's disease | Students |
| Tues | Jan 28 | 2.1 | Sequence Alignments 1
How Do We Compare Biological Sequences?
from Bioinformatics Algorithms: An Active Learning Approach
Note: We will be joined by H112 students for this class period. | Volker Brendel |
| Thur | Jan 30 | 2.2 | Sequence Alignments 2
MIT video: Local Alignment (BLAST) and Statistics | Volker Brendel |
| Tues | Feb 4 | 2.3 | Sequence Alignments 3
MIT video: Global Alignment of Protein Sequences (NW,SW, PAM, BLOSUM) | Volker Brendel |
| Thur | Feb 6 | 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 11 | 3.1 | Always check your answers ...
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 | Volker Brendel |
| Thur | Feb 13 | 3.2 | 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 18 | 3.3 | Evolutionary Processes 3
GBE article on lungfish development
EBI MSA Tools
EBI MP Tools
... a bit of history | Volker Brendel |
| Thur | Feb 20 | 3.4 | Quiz 3 | Students |
| Tues | Feb 25 | 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 | Feb 27 | 4.2 | Genome Characteristics 2 (Assembly) ... continued
Visit to the IU Center for Genomics and Bioinformatics for a demonstration of DNA sequencing technlology
(we'll walk over to Myers Hall 162 to meet there at 11:55am)
Sanger sequencing
Illumina sequencing
nanopore sequencing | Volker Brendel |
| Tues | March 3 | 4.3 | Genome Characteristics 3 (Assembly) ... continued
NCBI Assembly Help
paper wasp genome page
Other types of assembly: RNA-Seq | Volker Brendel |
| Thur | March 5 | 4.4 | Quiz 4 | Students |
| Tues | March 10 | 5.1 | Genome Annotation: Introduction
NCBI Genome: Deinococcus radiodurans
GFF3 standard
Review: Conditional Probability
GeneMark.hmm prokaryotic
GeneMark article | Volker Brendel |
| Thur | March 12 | 5.2 | Guest presentation
Bioinformatics support at IU: an introduction to RNAseq de novo assembly | Drs. Tom Doak and Craig Stewart and Carrie Ganote
National Center for Genome Analysis and Support (NCGAS) |
| Tues | March 17 | | Spring Break | |
| Thur | March 19 | | Spring Break | |
| Tues | March 24 | | Extended Spring Break | |
| Thur | March 26 | | Extended Spring Break | | |
| Tues | March 31 | 5.1 | Hidden Markov Models: Concepts and Algorithms
Hidden Markov Models
(from Bioinformatics: An Active Learning Approach)
GENSCAN
Profile Hidden Markov Models
TagDust | Online Class
Volker Brendel |
| Thur | April 2 | 6.2 | Protein Structures 2
peptide bond
Ramachandran plot ... very nice visualization thereof
(thanks to Prof. Eric Martz)
MIT Lecture: Introduction to Protein Structure; Structure Comparison and Classification
MIT Lecture: Predicting Protein Structure | Online Class
Volker Brendel |
| Tues | April 7 | 6.3 | Protein Structures 3: Secondary Structure
2struct server
Stride
Jpred - secondary structure prediction
SPIDER2
Genetic variation
NCBI dbSNP How To
NCBI dbVar How To
1000 Genomes Project Nature 491:56
Example: rs1131769
Recent paper of interest | Volker Brendel |
| Thur | April 9 | 6.4 | Quiz 6 | Students |
| Tues | April 14 | 6.5 | HMMer
PFAM
Protein Structures 4
MIT Lecture: Predicting Protein Interactions | Volker Brendel |
| Thur | April 16 | 6.1 | Protein Structures
peptide 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 | Online Class
Volker Brendel |
| Tues | April 21 | 7.1 | Gene Expression Analyses
from Bioinformatics Algorithms: An Active Learning Approach
MIT Lecture: Gene Regulatory Networks | Volker Brendel |
| Thur | April 23 | 7.2 | Gene Expression Analyses, cont.
Course Questionnaire | Volker Brendel |
| Tues | April 28 | 8.1 | Review: Assessment
sample paper
Sensitivity, specificity, and all that | Volker Brendel |
| Thur | April 30 | 8.2 | Review
| Volker Brendel |
| Thur | May 7 | 12:30pm - 2:30pm | Final Examination | Students |