INF 389 - Selected topics in bioinformatics fall 2010:
Bioinformatics for high-throughput sequencing

Curriculum

Lectures

• on most Tuesdays (1015-1200 in room 5118 - CBU seminar room) and
• on selected Fridays (1015-1200 in room 2104).

• Tuesday Aug 24th: initial meeting handouts
• Tuesday Aug 31st: Introductory lecture, planning the course handouts
  Papers:
  • Shendure and Ji: Next-generation DNA sequencing
  • Margulies et al: Genome sequencing in microfabricated high-density picolitre reactors (including supplementary material)
• Tuesday September 7th: Pyrosequencing, metagenomics introduction handouts
  Papers:
  • Kunin et al: A bioinformatician s guide to metagenomics
  • Wooley and Ye: Metagenomics: Facts and Artifacts, and Computational Challenges
• Friday September 17: Metagenomics II - handouts
  Papers:
  • Qin et al: A human gut microbial gene catalogue established by metagenomic sequencing
  • (Yooseph et al: The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families)
• Tuesday Sept 21st: Modelling pyrosequencing data - hand-outs, slides
  Paper:
  • Balzer et al: Characteristics of 454 pyrosequencing data - enabling realistic simulation with flowsim
• Friday Sept 24th: Genome variation, slides
  Papers:
  • Ng et al: Exome sequencing identifies the cause of a mendelian disorder
  • Biesecker: Exome sequencing makes medical genomics a reality
  (full papers are on the portal (minside)
• Tuesday Sept 29th: lecture cancelled
• Tuesday Oct 5th: primary data anlysis for the Illumina Solexa sequencing platform: handouts
  Paper:
  • Whiteford et al: Swift: primary data analysis for the Illumnia Solexa sequencing platform
• Friday October 8th - Solid technology and re-sequencing application slides (solid)
  Papers:
  • McKernan et al: Sequence and structural variation ..
• Friday October 19th - detection of structural variants - slides
  Papers:
  • Korbel et al: Paired-end mapping reveals structural variation, Science 2007, and supplementary
• Tuesday October 26th - 1000 genomes project slides
  Papers:
  • Via et al: 1000 genomes project, Genome medicince 2010
  • Weigel and Mott: 1001 genomes project, Genome Biology 2009
  • Ossowski et al: sequencing natural strains of Arabidopsis thaliana, Genome Research 2008
• Friday October 29th - finishing 1000 genomes project, RNAseq - slides
  Papers:
  • Siezen et al: Prokaryotic whole-transcriptome analysis: deep sequencing and tiling arrays, Microbial Biotechnology 2010
  • Bullard et al: Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments, BMC Bioinformatics 2010
  • RNA-Seq: a revolutionary tool for transcriptomics, Nature Rev Genetics 2009
• Tuesday Nov 2nd - small RNAs - slides
  Papers:
  • Taft et al: Tiny RNAs associated with transcription start sites in animals
  • Taft et al: Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans
• Friday Nov 5th - bioconductor package - slides, material
• Tuesday Nov 9th - de novo assembly (presentation on the board)
  Papers:
  • Myers: A whole genome assembly of Drosophila (celera assembler)
  • Zerbino and Birney: Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
• Friday Nov 12th - data representation and Galaxy demo slides (see also notes)
  Papers (the first most important for the exam)
  • Field et a. MIGS specification
  • Li et al: MAP format and SAMtools
  • FGED consortium: MINSEQE
  • Kottmann et al: GCDML
  • Blankenberg et al: Mainipulation of FASTQ data with Galaxy
  • Shumway et al: Archiving NGS data
  • Leinonen et al: The European nucleotide archive
• Tuesday Nov 23rd - bio-case / global ocean sampling - slides
  Papers:
  • Rusch et al: Sorcerer II
  • Seshadri et al: CAMERA
  • Goll et al: METAREP
• Friday Nov 26th - 3rd generation sequencing and future aspects slides
  Papers:
  • Kahvejian et al: What would you do if you could sequence everything?
  • Schadt et al: A window into third-generation sequencing