Introduction to Bioinformatics (3 CR)

I519/I617, Fall 2013
Instructor: Yuzhen Ye, School of Informatics, Indiana University, Bloomington
Association instructor: Michael Gough
Class meets: MW 9:30-10:45AM (Informatics West, I107)
Lab meets: F 11:15-12:30AM (Informatics West, I109) (links)
New office hours: M/W 1:30-2:30PM (Michael Gough; Info "Collaboration Area"), F 10-11AM (Pritha; Info West 010); Th 1:30-2:30PM (Yuzhen Ye; Lindley 301G)

  • Topics & schedule


    Week 1
    Aug 26 (M) Overview of I519 & Introduction to Bioinformatics slides (handout)
    Chapter 1 (The Nucleic Acid World)
    Chapter 2 (Protein Structure)
    [Primer] Molecular biology primer
    [Opinion] The real cost of sequencing: higher than you think! (2011)
    [Paper] Biology: The big challenges of big data (2013)
    Aug 28 (W) Algorithm basics slides (handout)
    Aug 30 (F) Lab 1: Linux, Genbank, and FASTA
    Week 2
    Sep 2 (M) Labor Day; NO class Chapter 3 (Dealing With Databases)
    Sep 4 (W) Introduction to programming with python slides (handout)
    Sep 6 (F) Lab 2: Hands on Python
    Week 3
    Sep 9 (M) Sequence comparison (and edit distance) slides (handout)
    Chapter 4 (Producing and Analyzing Sequence Alignments)
    [Primer] What is dynamic programming
    Sep 11 (W) Cancer Bioinformatics (by Thompson N. Doman from Eli Lilly) slides
    Sep 13 (F) Lab 3: Hands on R Slides: Introduction to statistics in R
    Week 4
    Sep 16 (M) Pairwise sequence alignment: scoring matrix & local alignment slides (handout)
    Chapter 5 (Pairwise Sequence Alignment and Database Searching)
    Sep 18 (W) Sequence database searching slides (handout)
    Sep 20 (F) Lab 4: BLAST, BLAT and RAPSearch
    Week 5
    Sep 23 (M) Multiple sequence alignment slides (handout)
    Chapter 6 (Patterns, Profiles, and Multiple Alignments)
    Paper: Issues in bioinformatics benchmarking: the case study of multiple sequence alignment
    Sep 25 (W) Clustering algorithms (UPGMA and others) slides (handout)
    Sep 27 (F) Lab 5: MSA tools (ClustalW & MUSCLE)
    Week 6
    Sep 30 (M) Phylogeny slides (handout)
    Chapter 7 (Revealing Evolutionary History)
    Chapter 8 (Building Phylogenetic Trees)
    Oct 2 (W) The tree of life (gene trees & genome trees)
    Oct 4 (F) Lab 6: Inference of phylogeny (PHYLIP & MEGA)
    Week 7
    Oct 7 (M) Sequencing techniques & NGS slides (handout)
    Chapter 9 (Revealing Genome Feature)
    Paper: Insights into the phylogeny and coding potential of microbial dark matter (Nature, 2013)
    Paper: Next-generation sequencing transforms today's biology
    Paper: Initial impact of the sequencing of the human genome
    Primer: How to apply de Bruijn graphs to genome assembly
    Oct 9 (W) Genome assembly slides (handout)
    Oct 11 (F) Lab 7: Assemblers (Phrap & Velvet)
    Genome browsers (UCSC genome browser)
    Week 8
    Oct 14 (M) Gene finding slides (handout)
    Chapter 10 (first part--Gene Detection)
    Paper: What is a gene, post-ENCODE? History and updated definition
    Primer: How do RNA folding algorithms work?
    Oct 16 (W) ncRNA discovery (& RNA folding) slides (handout)
    Oct 18 (F) Fall break; NO lab
    Week 9
    Oct 21 (M) Review
    Oct 23 (W) Midterm
    Oct 25 (F) Lab: Glimmer and GENSCAN
    Week 10
    Oct 28 (M) NGS applications: RNA-seq slides (handout)
    Oct 30 (W) Indexing techniques slides (handout)
    Nov 1 (F) Lab: BWA and Bowtie2
    Week 11
    Nov 4 (M) NGS applications: Genomic variants and epigenomics slides (handout)
    Paper 1: Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs(slides)
    Paper 2: Accounting for technical noise in single-cell RNA-seq experiments
    Paper 3: GIIRA - RNA-Seq Driven Gene Finding Incorporating Ambiguous Reads(slides)
    Paper 4: SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data (slides).
    Nov 6 (W)
    Nov 8 (F) Lab: samtools
    Week 12
    Nov 11 (M) NGS applications: Metagenomics slides (handout)
    Paper 5: Reliable Identification of Genomic Variants from RNA-Seq Data (slides)
    Paper 6: Genome-wide localization of protein-DNA binding and histone modification by a Bayesian change-point method with ChIP-seq data (slides)
    Paper 7: Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold (slides)
    Nov 13 (W)
    Nov 15 (F) Lab: MEGAN
    Week 13
    Nov 18 (M) Protein bioinformatics & structural bioinformatics slides (handout)
    Chapters 12, 13 & 14
    Nov 20 (W)
    Nov 22 (F) Lab: PDB viewer & Modeller
    Week 14 Happy thanksgiving!
    Week 15
    Dec 2 (M) Functional annotation (by Predrag Radivojac) slides (handout)
    Review: A (not so) Quick Introduction to Protein Function Prediction (download).
    Chapter 15.2
    Dec 4 (W) Proteomics (by Haixu Tang) slides (handout)
    Dec 6 (F) Lab: Gene ontology & graphviz
    Week 16
    Dec 9 (M) Biological networks and systems biology slides (handout)
    A poster on systems biology
    Dec 11 (W) Group project presentations
    Dec 13 (F) Lab: Group project presentations (Cont.)
    Week 17 Final week: final report due

    Bioinformatics program at IUB